When opening a container, corpse, or something where the Loot Menu opens, it cannot be closed without choosing the "R" option to Loot All.

This means, if you loot only one of two items, the menu will not close. If you loot all items individually, it will not close. There is no button (including Esc, I, etc) that will close the menu at this point, not even the "R" option. You must place something back into the loot menu, and then choose "R" to loot all.

Seriously? Something so fundamental to the game experience is overlooked?

Apparently you overlooked the TAB key.

Tac

I'm having the same issue, looks like if you rebind 'e' or 'r' to movement keys, the corresponding loot menu hotkeys break

TAB does work to break you out of the menu at least