Is theTOM/STP a make-or-break part? It's really not that great of a bridge. Plenty of better units exist. Plus, the TOM doesn't have individual saddle height adjustments, so you can't compensate for different neck radii. You need to have an 18" bridge radius to work with a Warmoth compound radius neck, and there's no such thing as a TOM with that dimension.
Also, is the body you picked out etched in stone? Because if you order it custom rather than from the Showcase, you can get your pickup cavities routed for whatever pickups you want, and you could still use the TOM/STP bridge as they can route that to be recessed. It would eliminate the pickup height problem, but you'd still have radius match-up problem. You'd never have an optimal setup.
If this is your first rodeo, I'm not sure you want to jump through as many hoops as you're setting yourself up for. Best to get parts that are designed to work together.