The factory MC would support the calipers. Hydroboost is different than vacuum type boosters. Where Ford used a different size for each vacuum brake setup, they only used 1 MC for the differenve brakes with hydroboost. 1” for 96-98 and 1 1/16” for 99-04.
your stock 99-04 calipers actually have less piston surface area than the ATS brembos. So changing to the 43mm rear calipers would still be around what your stock setup was in terms of surface areA. So yes, it would work with the MC
as to it the bias would be correct? I cannot answer that. Do you actually have a front/rear weight bias? Or just making assumptions as to how the vehicles weight has changed? If you are using the rear GT brakes, The bias is probably still fairly front heavy even if you’ve added weight up front. You might want to consider the Ford M-2300-M kit in addition to the 43mm rears. That bias would be pretty close to stock.