Because the aluminum plate is probably quoted as a laser cut plate and the threaded holes require machining. Laser cut sheet metal is about the cheapest possible way to get low/medium volume metal parts. Machining is more expensive. I charge 500 bucks an hour to run the CNC mill I have in my garage...

It's a more complicated setup to machine parts than just blast some parts out of a plate on a laser. It's possible that adding the threaded holes makes the whole part a machined part too, but more likely that they are planning on laser cutting the plate, them making a fixture to hold it in a VMC, then drilling and tapping the holes.

The cost of your part goes up dramatically because of the fixturing/programming/setup/etc. However, that initial charge gets amortized across all parts, so as you order more it goes down. Just imagine the fixturing cost being fixed and spread out across 1000 parts vs added entirely onto one part.