Its not fully compatible, there's some omisions.
The original game should be fully completable.
For Portals, tibet5 (I think it was) has a rotatey thingie that 'ejects' a puzzle piece. In FTE, that item isn't ejected and you need to noclip into the wall to collect it in order to finish the map/game, it becomes visible but its not far out enough to be grabbable. Its next to a rotating cog type thing on the ground, noclipping anywhere else is cheating!
I know of no other fatal issues.
I generally don't play through hexen2 that often, and quake-related tweeks have a moderate chance of breaking hexen2 thus other issues are more likely to appear without getting spotted/fixed for a while.
There's some particle effect omisions still, fountains come to mind, as well as snow/rain regions.
Deathmatch isn't well tested at all.
For many people, just one show-stopper is enough to, urm, stop the show.

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