Matt,
I have a hard time understanding why a new irrigation system would result in more drain covers.
As to the Sub Air system, I think Faldo's assertion would be wrong. Sub Air sucks moisture out of and pumps air into green tiles. I have never heard it used to suck water out of drain pipes, and if those need the water sucked out, then they must not flow on a gravity basis as designed.
I don't think its a sign of anything other than good construction - if the ball is rolling to the basin, it must be in the low spot as intended!
It does say something about the architecture, and more specifically, the need for a lot of basins when draining a flat Florida swamp when turning it into a world class golf course, and right at sea level so they could save the trees, a la Tom Doak's recent post. And, as I mentioned, TPC was a surprise to me when I saw how many basins were in the fairways, but I did understand them. And the news reports talk about how they wanted this thing well drained for their "5th major" no matter how much it rained, so it appears they put in a lot of drainage.
The alternate original design option would have been to import mucho fill to raise fw's, crown them (which tour pros would also hate) and drain to the rough, where other catch basins would drain off. I have to wonder if placing the wet areas where spectators would flow was considered to be the lesser of two evils to pros dropping often on a course designed specifically for this tournament.
I don't recall this being a huge problem before, so I wonder if the problem is just now arising with the newest version of the drainage system. You get a lot of drainage pipe in a $24M renovation project!