Forget ISS and the Russians. Its the legacy design, inherited from Boeing's Pressurized Docking Adapter on Space Station Freedom. Originally, one of a pair next to each other on the end of Hab and Science modules (or nodes in earlier design), to fulfil the spec that two Orbiter-spec docks be available.
Okay, long story short:
The fact that concept artwork showed what turned out to be the docking adapter that was fitted inside the shuttle bay in real life, was, in these depictions, actually part of the docking adapter on the station, bugged me.
And the adapters depiction is not consistent. Unless you see that when NASA render it, its not usually present or is simplified (to short, straight etc). This also goes for any contractor not Boeing: all used simplified straight tubes.
It is important to remember that they were not making the docking adapter. When Boeing (and subcontractor McDonnell Douglas) render it (be it 3D, physical model or artwork) it shows the strange adapter. When you look at the artwork and the animations, then you see the origins of the PMA.
(Boeings design work actually began in 1988, with Work Package 4 on the U.S. Space Station Freedom)
They were PDA's and are angled opposite each other.
This matches with articles I read that the design, until the 1993 redesign, always specified 2 race track / parallel running modules (science and hab), and always must have two docking ports, to allow Space Shuttles be docked at either one.
Two ports are available at all times for Orbiter berthing, as specified in the system requirements.
(Conceptual Design and Evaluation of Selected Space Station Concepts, 1983)
And the ports must be shirt-sleeve walk through (ie. like moving from shuttle cab into spacelab). (there were drawings of spacelab being directly attached to the nodes of Freedom too).
And that spec went all the way back to the dual keel design. But that design had 'long boom' docking adapters, described as actively controlled load alleviation device.
The booms were both oriented to the left, as if keeping the shuttle slightly away from structures to the right side of the truss. In that design there are still the nodes, notably with the Cupola for overseeing operations, one on zenith, one on nadir.
When the redesign got rid of the nodes, the keel, and the long booms, the shorter PDA design appeared. A redesign later, the PDA orientation changed too, to being opposite each other, whilst retaining the nose up and nose down attitude of the docked Orbiters.
It looked like they were changing how the shuttles were docked and keeping them as far as part as possible without making the adapter go beyond the extent of the shuttle bay it would fit when launched, and at the same time not be structurally weak by not being too long.
The PDA's and therefore the whole docking assembly being rotated away from each other gave enough clearance to satisfy the specification that the station be capable of supporting Orbiters at either dock.
It also brought a benefit that the slight outwards alignment meant that the manipulator arm of the shuttle payload bay had more room to move modules out and on to the station. Given that the shuttle arm was only on one side, this makes sense to have the side with the arm on the outside.
Around 1992, construction of the station (Space Station Freedom Media Handbook) refers to an unpressurized and then pressurized system taking over. This system was called the Pressurized Berthing Adapter, which had a sliding latch for lining up, and then had the Pressurized Docking Adapter (kinked) as part of its assembly. This was based on the standard pallet integration that consisted of trunnions that engaged with the PRLA and keel of the Orbiter's Payload Bay, giving a hard dock.
The unpressurized berthing adapter extension, locking and attach
systems extend the unpressurized berthing adapter and latch and
structurally join it to the mobile transporter element, thus
providing the initial berthing interface between the orbiter and the
space station freedom. This sequence is reversed when the pressurized
berthing adapter is attached to the space station freedom and the
unpressurized adapter extension can be removed.
Collectively known as Pressurized Berthing Adapter.
Canada's Arm (Automatic Control in Aerospace 1992) was now part of the docking process, capturing and pulling in the Shuttle to mate with the PBA.
the scenario and initial conditions for a simulation of automatic
berthing of the Shuttle Orbiter to the Space Station Pressurized
Berthing Adapter. The motion is relatively slow in order to avoid
excessive excitation of oscillations in the SSF /SSRMS/Shuttle dynamic
system which has a natural frequency below 0.01 Hz. It takes about 15
minutes before the Shuttle is positioned within the capture envelope.
After the redesign dumped the twin module and twin docking adapters, the PDA's became PMA's and went solo, as depicted in later artwork, all the way to 1997.
Why still kinked?
My understanding is that they had already been designed and built by then.
So why build new docking adapters when you can still use the ones you made.
(Node 1 and PMA-1 and 2 were undergoing structural tests post fabrication, in 1996. Documents referred to the station as Alpha, a name from 1993, the PMA's in their current form already existed on the baseline SSF in early 1993)
PMA was a known structural article when Node 2 (before that was replaced by Node 1) was being tested in 1995.
Departments of veteran affairs and housing and urban development, and independent agencies appropriations for 1997
Today, there is more than 80,000 pounds of flight hardware that has been manufactured.
32 percent of flight hardware complete.
Node 1, PMA-1, PMA-2...
...Complete mechanical equipment installation into node structural test article (1st Qtr 1996)
Production of flight hardware continued in earnest during FY1995.
Boeing completed the primary structure for... node 1 and US laboratory. ..assembled the pressurized mating adapter.
(incidentally, they look like they could have fitted spacelab and attached to the internal airlock of the shuttle cab, as in a shorter, smoother tunnel than was used).
So, in short, when everyone has been trying to understand the kink, they have been looking at it from the wrong angle.
Turn the adapter 90 degrees and you see how it was originally designed to fit, along with a 'phantom twin' next to it. Nothing to do with loads too big, or space behind the shuttle cab, it was just Boeings concept of having two available docks at the same time. Payload Bay and arm clearance was a side benefit.
Nothing to do with hatch clearance either, these designs were from long before Russia got involved in 1993.
(As a side note, a study was done before the Russians signed on in 1993, for Soyuz to be used as a CRV. Multiple options were looked at, each using a PMA for the Soyuz to be docked to. The study for this exists based on a pre-existing base-line SSF configuration, that already had slanted PMA's attached, so this was never the origin for the PMA's, they were already designed that way) https://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/19940012599.pdf
Dual Orbiters docked simultaneously was considered and tested for, but the Station ultimately proved structurally incapable. What is visible is the clearance designed for future craft docking given by rotating the PDA's 90 degrees, perhaps eventually simultaneously.
From Space Station On-Orbit Assembly and Operation, 1991, you can see how the Space shuttle is berthed using the Space Station Remote Manipulator System, and when docked using the combination of Pressurized Berthing Adapter and Pressurized Docking Adapter.
Note that the PDA is rotated to the side.
For a short time in between Space station Freedom and International Space Station, there was another name.
In 1993, President William Clinton called for the station to be redesigned once again to reduce costs and include more international involvement.
The White House selected the option dubbed Alpha.
In its new form, the station uses 75 percent of the hardware designs originally intended for the Freedom program.
Anyway, that's my take on it until someone from Boeing/MDc says "No..." ...
space station ref artwork:
1997 image showing slanted PMA