Why? I can only take some guesses. The only person who can really answer your questions is the engineer.
Possible Reason #1
MIDI data is easier to work with that audio data. The engineer was ensuring he captured data in a format that he could easily manipulate after the fact. Far easier to fix a miss hit by moving a MIDI note around than it is to re-track an entire section or performance.
Possible Reason #2
Triggers are easier to setup than mics. For sure mic'ing a drum kit falls in to the category of "it's an art and a science". It's a daunting task. It requires more than a few mics and in some cases (like mic'ing a kick) some speciality mics are really called for if you want an excellent outcome. Could be the engineer didn't have the know how to mic a kit up or the time or the studio was lacking the gear it needed to capture a full kit adequately.
Possible Reason #3
You don't have to deal with bleed. Triggers are mostly independent, and even if you do get a trigger mis-firing it's an easy thing to just delete the MIDI note.
Possible Reason #4
You don't need a lot of knowledge to mix a great sounding kit if you work with triggers. I realize this is counter to what you're getting from this studio and I'll admit this sounds like a problem with the samples they're using or perhaps the skill of the engineer with the software. I definitely have cut some great sounding drum tracks where the drummer was playing a V-Drum kit, run in to a Alesis Trigger|IO module, and triggering a BFD 2 for the sounds. The sounds in that VSTi are captured so well, and already EQ'ed and tweaked so nicely, even a drum-mic'ing and mixing neophyte like me can get big, beautiful drums out of a setup like that. Could be the engineer was trying to hide some lack of still here when it comes to dealing with drums during mixing.
Those are just some reasons he might have insisted on triggers. I'll admit they don't make a lot of sense. You should definitely take up your issues with him. You were footing the bill and these sorts of decisions should be yours, not the engineers, to make.