I had done a little poking around on the F150 boards a while back to get a deeper insight to the Ford BMS system. First of all, the consensus with them with battery swaps of an increased capacity is to use FORScan to find and pick the closest battery size that matches. There's only a finite number of choices that can be made within the BMS system.
Another thing they do and I did too to an extent is change the SOC target %. I had noticed through various methods (lighter socket, OBD data, etc.) that the voltage of the charging system would vary quite a bit. As SOC quickly got to target, the voltage would drop off a lot (down in the low 12's at times). It would then only go up to a normal voltage amount if coasting or braking. I chalked this up as 'intelligent' or 'efficient' charging. Something I'm familiar with in my experience with BMW's (they ran into a lot of battery issues as a result 10-15 years ago. Now they charge at a constant 14.8v). This created a few electrical accessory issues for me (console fridge, stereo amplifier, etc.). I played with SOC targets until I finally settled at 100% and get better numbers now (avg. 14.4v). I have seen the F150 guys go so far as to target 110% as I'm sure this drives values up to 14.8-14.9v (this is OK). More voltage - within reason - is less amperage draw. A good thing.
