So they put it through the flat roof, through the deck… No I dont know why…
I would trip over it, for sure !
No way to run horizontal below the roof?
Now if the cut it off and put a flange on it they can mount the toilet! 
What a view!! :mrgreen:
Is the roof material designed to have deck on it? Will the roof withstand the live loads (no pun intended). Sounds like a bigger problem, IMHO.
The believe the structure is strong enough, It had rubber roofing installed on the semi flat roof. I informed the client they would need to keep it mostly shoveled off in the winter. No signs of leaking whatsoever. It MAY have been possible to rout this to the side, but probably not without cuttng apart an IMACULATE bedroom ceiling. My guess is the vent came first, then the deck.
Should smell real nice up there on a hot summer day.