Large diesel motorhomes either have a generator in the rear side compartment or up front in a slideout.
Space is an issue, and from quite a few years rv'ing I've seen rigs with and without separate starting batteries.
Because a 40-45 foot motorhome is so long, yeah the runs from battery compartment all the way up to front are problematic, which
is why many slide out front gens have a separate starting battery. The idea of a having a dedicated strong starting battery just for your generator
is a good one, if layout allows.
Some battery compartments are closer to the front, under the entry steps. Some are wherever they find room for the batteries.
The OP's set up sounds like a normal motorhome. Having a dedicated deep cycle battery bank just for house power is ideal, and a separate
battery just for the gen.
In my old boat I had a switch that would connect one bank of 4 8V batteries to the second identical bank, 12V and 32V system.
Lot of batteries. But if one engine wouldn't start due to low batteries, a flip of the switch and the second bank took over.
I wonder if the OP has any such little switch in there. One hopes the setup is bone stock. If the prior owner started "customizing", you
have even more detective work to do. Every connection is a point of failure, but I think by now OP is used to taking every single thing
apart on that motorhome. Sounds like me rebuilding a boat. Everything is suspect, you trust nothing.
With more sleuthing and diagnosing, I'm sure he'll get it.