The biggest difference will be in weight distribution. The larger spur/pinion combo will move the motor forward in the chassis. I haven't tested this myself, but in theory it would provide less rear grip and maybe a tad more steering.
The smaller combo will have less rotating mass for faster acceleration. But the difference will probably be too small to notice.
I would suggest using the larger combo for finer ratio changes to better dial in gearing at the track. I currently use a 120t/64p spur (same as 90t/48p) with a 2.5mm chassis on carpet, even though it sticks out the bottom slightly, and I will probably switch to a 124t with a 3.0mm chassis for even finer ratio adjustments.
