I'd assume this could be possible in terrain builder to create a diagonal "sink hole" then pretend thats a tunnel, and build your facility into the side of a hill or something since it would all need to be above sealevel.

Being able to do things like trenches and stuff without them being above ground would be nice, but I don't think its possible with how far the engine has evolved already (RV needs to go into retirement after they're done with A3 and DayZ in my opinion), alot of the code for handling terrain is probably burried real deep, and it would be a hassleto rip it all out to redo it.

indeed, but if we could take full advantage of the new Enfusion engine, it could be done.
after all dayz, is a hybrid of old and new technology, it would be enough to pass it has 100% on the new engine Enfusion with which I think the creation of tunnel and under ground and possible.

sorry for my English.