noesteijver we've done quite a bit of refactoring in the AAM 6. It actually was completely rewritten. The only place we almost did not touch is the UI (I wish we had capacity to rewrite it to be ReactJS app).
All the mentioned above capabilities are obsolete. They are no longer in use. More particularly the allow_ajax_calls capability was removed because it was causing quite a bit of issues for themes and plugins that use legacy
/wp-admin/wp-ajax.php endpoint. The only capability that you need to worry about is aam_access_dashboard if you need to manage access to your backend area.
Keep me posted if anything.