I'm pretty sure I've seen every X-files episode, and I watched all the new ones. I'm as able to suspend disbelief as well as anyone, as long as there's a certain internal consistency within the make-believe.
Moreover, working at the VA during my surgical residency, I've seen men with tracheostomies from their throat cancer due to cigarettes, smoking through their stomas.
But this, CSM smoking through his trake while talking normally? Not a thing. Anatomically. It's not a thing. You can talk, you can inhale normally. You inhale through the hole, you can't talk. Not a thing.
That is all. Except for the ending.