I would suggest removing the option to have no second stack.

Let's focus on convenience without changing the game itself. I personally get annoyed when both heroes have only 1 stack each in Castle mode, but having to approach the arena or the Vault, and negotiate options, especially before a battle, is not something I enjoy. Even here, there is no consensus on whether these checkboxes are needed or not.
Another question: how difficult would it be to make the patch work with regular saves in normal mode? The idea is to avoid having to turn it on and off every time, and to remember whether you are playing with it or without it. At the beginning of the game, on the options screen, add a checkbox at the very top "(do) not use the patch at all, play in normal mode". And in the save names, put some kind of mark to distinguish the patched ones.
Users, who is for/against?

Added 3 minutes later
Regarding hotkeys: in Heroes of Might and Magic 2, there was a very convenient feature when selecting a chest: Enter - take the money, Esc - refuse, gain experience. I still miss it