Yes, IME tapering on the ball end/bridge side helps reducing the low-B mudiness on the higher fret notes. AAMOF, I prefer to use tapered low-B too and I've swapped the stock EXL170-5SL (non-tapered low-B) on my EHB1005MS (the long scale one) to NYXL 45-105 set and a tapered NYXL 130T low-B. But, if I use a lighter low-B (125~120), I'm fine with a non-tapered low-B.
I just never own/play a short scale with a low-B, so I know nothing about this combo.
can't argue on that...
In regards of putting on a 135 low-B, I've used it several times on a few Ibanez basses. None needed nut modification.
just occured in my mind, maybe...
since there are 3 tapered strings (B-E-A) out of the ProSteels EPS300-5 set, which includes the A string that the OP is having a problem. And, the fact that tapering makes those strings flex more a little bit on the saddle side. Also, given that these strings are being put on a short scale bass which strings are already relatively lower tension and became more flexible...
maybe... the strange mid on the 3-7 fret range of the A string perplexing the OP is caused by the string being too flexible.
just my 2¢...