I have the same issue, and I also have the Boeing's offical performacnce software data and FPPM to back up that TOPCAT's data is mostly correct (it actually use the FPPM data).

Yesterday I takeoff on 752wP2040 from LGRP with 98.5T,Flaps5 and 48C ATM (FPPM shows I can go 52, but FMC only allow 48max), I used up the full runway (ther should be at least 15% margine for all engine takeoff)

Also the cruising EPR is about 0.1 higher than the manual. while FF is around correct value.

While the RR engine have faulty FMC ATM EPR cauculation (as I reported in bug report post), if use the correct EPR from FPPM, the takeoff distance and climb performance feels about correct.