I had a feeling this was the answer. Both suggestions are ultimately variations of create-compensating-transactions that I described. Your second answer is the same as what I originally mentioned - make manual Bank Transfers at some interval from the parent into the subaccounts.

Out of curiosity for a more general scenario, let's say a business (nonprofit or for-profit) has two completely separate checking accounts at separate banks. Again, one Sales Receipt to a customer for a combined total that has to be split-deposited. Apparently the general answer is "QuickBooks cannot split a Sales Receipt into multiple Bank Deposits". So at some point, as you mention, you're going to have a transaction mismatch on the downloaded bank account deposit transactions that you just have to not match and ignore, because the workaround is to create only one Bank Deposit, to one of the bank checking accounts, with a compensating line item to simultaneously "deposit" into the other bank checking account.