Hi James - just to explain the two extra methods you note in Sales & Purchases as they are substantially different to the Bank ones.
These are designed for payments on account. In other words if someone sends you money up front, before an invoice, or you pay a supplier a deposit against a future bill, you can use these two methods to park the money waiting for the invoice or bill against which you can allocated them. You can see the money, and do the allocation, in the "unallocated cash" section in the Money menu. Some people also use this facility for overpayments.
Having said all this there are certain technical difficulties in using this area of the software, the main one being that it does not account for VAT, so should not be used for VAT registered businesses.
I take your point that if, from the bank screen, you have chosen Money in, you should go to a Money In screen, but the reality is that the system only has one "Manage Money" page and so, the smallest redevelopment would be to only have one link on the Bank screen "Money in/out". Development time is very valuable and so keeping changes as simple as possible will give them more chance of success.