On its face, 3.25 versus 3.23 is less than half a percent difference, so based on diff alone those two should be ignorable.
When you did your motor swap, you also swapped the transmission. The gearing on the E36 transmission is very different from the E30’s transmission. So to be accurate for comparisons, you’d need to take both into consideration.
E30 325is with diff = 3.73
(assuming Getrag 260/5 transmission)
First = 3.35 (*3.73 = 12.50)
Second = 2.03 (*3.73 = 7.57)
Third = 1.36 (*3.73 = 5.07)
E36 M3 with diff = 3.23
(assuming ZF 5 speed transmission)
First = 4.20 (*3.23 = 13.57) ==> 8.6% increase
Second = 2.49 (*3.23 = 8.04) ==> 6.2% increase
Third = 1.66 (*3.23 = 5.36) ==> 5.7% increase
So you are getting way more bang for your buck with the 3.23 diff and your shorter gearing on the E36 transmission than you had for the E30 one with the shorter diff.
So only looking at the diff ratio in isolation you get a completely bogus view of what is happening from the flywheel back.
Whenever there is a driveline change like this to put a bigger motor in a lighter car (and associated gearing stuff), I have to wonder whether it makes more sense to treat the car as the chassis it started as with a power and gearing upgrade, or to take the bigger car as the baseline and then add points to it for the “effective” weight reduction. Neither one seems like an accurate model.
We would be well served by looking at actual run histories for cars with certain characteristics and determine the real-world equivalency for things. Our current points model is fairly arbitrary (I know Hal would strongly agree).