I was just watching The Right Stuff for the 100th time,and I've always wondered what is that hose spewing flame/burning propellant out of the bottom of the rocket. It's definitely not an engine,and why would the engineers have designed it that way. I have attached an image.
It's the turbopump exhaust from the booster (jettisonable) engines.
From Spacecraft and Boosters by Gatland p. 222-224
Exhaust stack discharges fuel-rich efflux outside reverse aerodynamic flow at base of missile
In other words, the main purpose of the long duct is to get the fuel-rich turbopump exhaust away from the bottom of the vehicle to prevent it being trapped there by recirculation and potentially igniting.
The sustainer engine turbopump exhaust goes into its nozzle instead using an "aspirator", you can see that duct marked #41 on the schematic.
It looks like there were several variants of the design over the Atlas program. There's lots of good information on this page including this schematic
and this photograph.