This is not something I really can help with, sorry.
Android has a general purpose "default app per intent" mechanism, Aqua doesn't do anything to get some sort of special treatment, and I've not heard about a third party "default app manager" until now...
You *should* be able to clear the defaults for the bulit-in Email app, and get prompted for mailto: links --- except I vaguely recall seeing some code in stock Email (stock Android code, I should mention) that handles clicks on mailto: links internally, not offering the choice of other apps.
So, clicking a mailto: on a web browser page, etc -- *should* show a prompt. Clicking a mailto: link in stock Email won't, and it's how stock Email is.