The Dragonfly cruise stage looks rather similar to Curiosity's cruise stage, so I've looked at Curiosity. Curiosity's backshell contains a hatch. This was used to install the RTG at the last possible moment (a few days before launch, long after the rover had been packaged in its backshell plus heat shield.
Here is Curiosity's backshell being prepared for encapsulating the rover. You can see the hatch.
The MMRTG won't be installed until just a couple of days before the launch, because it throws off so much heat. Once the rover has launched, a cooling system will vent the excess heat to space, but between now and then it takes a pretty powerful cooling system to keep the MMRTG from heating up the interior of the spacecraft to hazardous levels. I was told a while ago that they have three redundant cooling systems working to keep the spacecraft at a safe temperature between MMRTG installation and launch.
For Curiosity, this means the RTG must be installed so it's accessible from the backshell. If it were installed horizontally, the hatch would have to go through the heat shield, and that's something spacecraft designers try to avoid as much as possible.
In the drawing you can see Dragonfly has the same packaging issue: if the RTG were horizontal, the hatch would have to go through the heat shield.