I generally add custom application shortcuts to XFCE's keyboard preferences instead of i3's config and change i3's $mod to the Alt key. Haven't had any problems of conflicting shortcuts.
I much prefer having window management stuff on super since I use a lot of terminal apps where alt is important. Can't overload too much there or things get funky. And I have a lot of custom window management keycombos for i3 because the basic set are a bit bare.