i think there may need to be toggle options to hide each gui (player doll, inventory, coord, etc) when inventory is opened.

The hud being hidden while any inventory is open is an intended feature as it's the same in Console Edition. If you don't want this to happen there is a config option called "Hide Hud In Container".

Gui enhancements offered by this mod like the paper doll and coordinate display are also hidden with said option enabled.