Macaroon is actually dead, as it was not updated for the API changes in WoW 5.0.
Maul started writing Ion from scratch with the intent that it would replace Macaroon, but ended up not having time to finish it, and based on the lack of updates, still doesn't have time to work on it. He's posted a couple of "sorry I've been really busy, hopefully I'll have time soon" type things but either he's still really busy, or just lost interest in the project. I wish he'd just updated Macaroon for the API changes instead, but
c'est la vie.
As for the Bartender issue, I believe it stores keybindings along with the Blizzard ones, so checking the "per character keybinds" in the Blizzard keybinding UI might solve the issue. If not -- I'm not sure if Blizzard supports separate keybinds per spec -- you might need to use an addon like
RespecBindSaver, which will work with the Blizzard keybinds, and all addons that store "real" bindings (which are saved between sessions in the bindings-cache.wtf file) instead of "override" bindings (which are not saved between sessions and must be re-applied by the addon at login; this is the method Ion uses).