"As an aside, the Calder book explains that one large battery bank is more efficient than two smaller battery banks. ..."
This is technically correct, but Peukert's law which underlies this is insignificant for many applications...when typical loads are low, like refrigeration and toilets for example. Most other design components are MORE significant. It becomes more important for high current steady load applications.
I have always split my house load between two banks...hence efficiency is theoretically equivalent to a single bank with loads combined BUT....if one bank goes accidentally dead, say to a refrig door left open, or a failed water pump motor, I have not lost ALL my accessories....
for eample I run a 12v frig off one bank, a 12volt freezer off another...about equal loads, and I have maintained some redundancy....
it's a far superior arrangement for those who cruise away from dockside power for long periods....loads can alway be switched from a dead bank if required....
That is one of the very few explanations from Calder that is just a bit misleading and not thoroughly informed..
not a good idea to put all your eggs in one basket....For example, I have 7 bilge pumps...three on one bank, three on another, and the last one on a third bank...and my separate bilge alarm is on the third bank..which should be the last one operating if disaster strikes...
If you do gain a 1% advantage, you'll quickly forget it when a single big bank goes dead....and mission critical loads fail to function....
"Would there be any harm or issues in keeping the two bank paralleled into one big bank while on shore power so that both get good charges, then unparallel them before starting so you maintain the redundancy of two banks while under way or at anchor?"
That's a good general approach....only if they are manually paralleled and you lose shorepower might both banks be drawn down together...