I used alcohol stoves fairly regularly for a few years, and no go between that & canister stoves. The fuel has never tainted food-it vaporizes before touching anything you would put in your mouth, and I ALWAYS cook with a lid on, due to the relatively low heat output, as mentioned. So, to set your mind at ease-it only smells bad before you burn it

As to using the brass lid on a trangia stove to put the flame out-remove the oring. Simple enough. I do this all the time with my trangia. Just make sure you put it in a pocket or something, so you dont lose it.