Thats it. Never tried the auto-loot but my minions blocking inventory on the ground really is annoying. Great game btw. Got the whole bundle today. 7 hours already...
As long as it's not a trap, you can walk into their space to switch places with them, then grab it from under your own feet (Shift-click is a bit quicker than dragging it manually). If it is a trap, yeah that gets awkward, walk away, then come back once they're safely behind you again. Glad you're having fun!
You´re right, it works that way. I never thought about it because it seems so counterintuitive. I normally run around and click on the items once they are in reach, not stepping on them. I think that is one of the small things that could make the game more accessible (hitting your minion accidentally by clicking too fast is a similar problem, simple idea: one click = change positions; double-click = attack)) If you already offer the alternative to play it with the mouse you may also make it equal, which would mean to be able to right-click fast pickup stuff like with shift+click.