When disabling items via config, or content disabler mod, it doesn't disable the associated achievements, and the game still loads the items, but makes it so they have no sources.

The disabled items will also show up as locked in the command menus

Yeah, sorry, can't really fix that at this point, because the mod allows you to turn items on and off in the main menu, so I can't make it not load items at all. Though, maybe I can think of some ways to disable relevant achievements.

As for command menus, it also happens with DLC items if you don't have the DLC enabled, so there's not much I can do.

I'll take achievements being disabled if thats possible, thank you for your time Mystic