Aside from the battery science thing
, I have found that whenever I check the state of charge of both batteries, the primary battery always has the greater charge, often by as much as 20% more. Both batteries were purchased at the same time, and there is nothing different between the two batteries except that the alternator charges the primary battery directly, and the secondary battery gets its charge via the long battery cable.
I do have a higher output alternator (I think 140 amps), but I don't think that makes a lot of difference. I suppose charging two batteries instead of one battery might lead one to want a higher output alternator, and that is supposed to require bigger wires to/from the alternator.