Location of transaxle coolers, exhaust design, and so on, can have an effect on underbody aero. Teams are free to place them wherever, so there are potential gains to be had.
DJRTP also seems to have additional bracing in their bonnets across the hump, that PRA does not. Suggesting that there might have been a flexing issue with the bonnet itself, that may be disturbing the aero.
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