Alternate materials - Ferro-fibrous armor slots and endo-steel structure - do not occupy critical slots so much as reduce the number of slots available in a given section. They should have no impact on gameplay whatsoever.
Heat sink placement, on the other hand, does. In my group back in the 90s, it was often a hotly contested topic wether they should be placed in the legs by default (to benefit from water cooling) or be used to pad out ammo crits in torso locations.
In this respect, official record sheets went a long way to stop players from bickering.
On the other hand, component placement on official record sheets still makes me scratch my head sometimes. Granted, art vs. stats mismatch are more a TRO problem. But in some refit cases the record sheet just doesn't match the fluff. Take the ZEU-6T: Fluff says refits are arms with a PPC and heat sink instead of the AC/5 that were shipped out to LCAF units, but in an apparent oversight the official record sheet doesn't place the heat sink in the arm (I forget where).