> As of fuel gauging multi cell batteries, maybe I can just fuel gauge the last one, the one with one terminal connected to GND and assume that all other cells are at the same level.
You can do it by whole battery voltage (it is simpler, than sense only one cell, and more precise), but only for LeadAcid and NiCd. LiIon has very flat discharge curve, so you can't say how much of charge in it only by voltage of battery. Fuel gauge IC literally count Coulombs flown in/out of battery.
> But then it comes to my mind, what if I build a battery pack with batteries that have different levels of charge? Won't the CC charging process damage the batteries that reaches first the full charge?
Yes, it could. That balancing circuits in BMS is made for. They take care of avoiding of overcharging of separate cells.