The traditional way of doing this is:
- Removing the item from the default toolbar set here: https://searchfox.org/mozilla-central/rev/c03e8de87cdb0ce0378c0886d3c0ce8bbf9dc44e/browser/components/customizableui/CustomizableUI.jsm#244-254
- Add a migration to put the toolbar back for users that have used the button before in here: https://searchfox.org/mozilla-central/rev/c03e8de87cdb0ce0378c0886d3c0ce8bbf9dc44e/browser/components/customizableui/CustomizableUI.jsm#244-254
- In that same migration, remove the item for users that have customized their toolbars but never used the item
The problem here is timing. You can think of a UI migration almost like a database migration, except we're writing to the toolbar customization pref rather than a database. Yes, it's reversible, but the reversing requires additional logic, and it's all very state dependant.
I think the simplest thing to do is make the migration one-way, and if people test Proton, and then disable the pref, make sure they're aware that the things that were removed are in the customization palette. The less simple thing to do would be to somehow realize that Proton had been flipped on, and then flipped off, and put everything back. I suspect that this is more trouble than it's worth.