A couple of things that might have influenced the choice...
Cam Timing Duration[ seat to seat] on the Race GT40's was ~ around 330°, when you factor in the max RPM of around 7000 on the SB & ~6500 on the FE the primary length ends up around 38/40 inches depending on where you want max torque etc so the ability of the crossover 180° design to 'soak' up a couple of inches would have been a +, ( nowdays with most people opting for shorter duration cams in the `~270/290° duration range along with higher RPM that means that most 180° setups are longer than ideal, but in header design longer is the safer option.)
The design of the rear of the tub & horseshoe also favours the up & over the transaxle setup, as getting the headers threaded thru the rear suspension links after exiting the engine recess would be an issue, also the height of the rear window plus need to get carb air from each side would prevent an 'up & back side for side' deal.
Interesting point, it appears the J-car that Ken Miles fatal accident occured in was tested with either eight seperate exh stacks or a short side for side system at one time, there is a photo of the rear body clip with cutouts that suggest such a system in the freidman shelby GT40 book.