1. I doubt it has ever occurred to the design team that anyone would ever want to remove every option on the main menu. Such an action renders the software inoperable by the expert user is is designed to be used by and would be a pointless exercise. I would imagine it behaving exactly as you describe should I decide to try it. I have no wish to.

2. Unless you accept the "Apply modified settings" prompt after each shortcut change, it may well not be stored. I have removed multiple shortcuts in a single edit session and as long as I "Apply", there is no loss of any of my changes.

3. Which version are you running? Mine behaves nothing like that. No, the developers have no such expectation of you.

Sorry you are having such trouble using the customisation features of TB. It certainly goes about such things in ways unique to itself and perhaps, if you find them too cumbersome, then this software is not the right one for you.

I would comment that customisation is very much a secondary function, one that you "set and let alone". There is nothing superior to TB when it comes to handling email, filtering, templates and address book; its primary function.