But I kind of plan on doing something similar with Aaron. Basically, he can put things in his inventory, which causes them to disappear from sight. Unfortunately, he can't access it outside of HQ or his home continuum (in part because his disguise covers his Pipboy). As far as his partner's concerned, this is some kind of strange, and potentially incredibly useful, magic; as far as he's concerned, it's perfectly normal. He also baffles her with his ability to effortlessly haul around 200+ pounds of gear and actually enjoy Cafeteria food (at least it's radiation-free).

Personally, I find the intersection between game mechanics and storytelling to be hilarious, probably as a side effect of reading Order of the Stick.

If it'd be funny or advance the story, yes. If not, you can hand wave it away.

You just have to remember that the character's actions make perfect sense to them. An example:

Partner: Why are you eating in the hallway?

Sim!Agent: Where else would I eat? The table is full of your stuff.

Partner: You mean the single book on the table?

Sim!Agent: Exactly! Clean up your stuff!