Under the "[ContainerUIActive]" heading is likely where you need to re-assign the R key to what you want, as it is currently assigned to something called "ReRollContainer".
DefUser.ini makes mention of it under its "[ContainerUIActive]" heading with this comment:
So what I've done is under that heading, the key that I've rebound to Reload (Shift) under default, I've bound to ReRollContainer under the [ContainerUIActive] heading.*
;NOTE: Reload disabled in this context in favor of ReRollContainer
But again, I don't feel like wasting time swimming away from the plane crash a 5th time, going down the elevator thing, etc. just to see if it works. As far as I know there's no developer console to re-execute changes to the User.ini file, so any time I make a change, that's what we are talking about to get back to testing.
Luckily, later today I'll have the full game installed which allows saving. This means I'll be able to get to a part in the game that I can test out container use and tweak the controls to my liking... even if it means I have to edit ini files by hand. Which I'd rather not do.
*My guess is that at one point there was a function to flip through the contents of containers with this ReRollContainer command which is now defunct as as far as I can tell, there can only ever be 3 things in a container of any kind, and when you hit the Use button you grab everything no matter what. I'd love someone to correct this if needed.