I'm an Electrical Engineer, let me see if this helps--
The limiting factor is the wire gauge. Batteries have internal resistance, wire has resistance. Beyond input voltage, your rate of charge becomes self-limited to a certain extent by the wire. At most, you will have a 4 volt difference between the alternator and the TC - this assumes fully dead TC batteries and a cold just-started alternator. Most factory truck-to-TC charging circuits are between 20-40amps. Given that you have multiple batteries, it would just simply take longer to charge them back up. The wire is the limiting factor - there's no regulator beyond what's on the alternator, and no other device besides a fuse to limit current.
A lot of us have multiple batteries (I have 6) and had the need for a better charging circuit. Like most, I've ran a dedicated 4ga hot and ground wire back to my TC batteries. I have put 100a breakers at both ends, the truck and the TC side, in the (hopefully) unlikely event of a short. A short will exceed the wire's rating and pop the breaker, because now you're going from 14.7v to 0---versus 14.7 to 10.5(dead TC batts).
That being said, the TC batteries have never popped the 100a breaker on either end. Now, if I upgraded to 2ga, 1ga, or even 0ga, it's entirely likely the 100a breaker could pop, because the wire can now support the higher current at that lower voltage differential.
