I don't think it's a problem with canister stoves, since there's no liquid involved and the fuel canister is self-sealing. I regularly store both the stove and canister inside the pot. (Many such kits, like the Jetboil, are designed to do that; given product liability issues, I'm thinking they wouldn't package it that way if there were any doubts.)

When I briefly used an alcohol stove, it was a Trangia, and the screw-on gasketed lid handled the problem rather neatly. However, I still put the "sealed" stove in a ziploc bag before putting it in the pot.

I never stored my white gas stove in a pot, even in a ziploc, for exactly the reason you state.

But that's just me - but I've been married a long time, so I'm used to being wrong.