At a guess, it is mostly a money/time issue. Making completely different multiplayer maps means coming up with textures, models, and ideas that will only be used for multiplayer. Basing the multiplayer maps around the single player resources means that they can recycle textures, models, and ideas.
Going by FPS from the previous generation, making completely different maps opens you up to questions like "This area looks cool. Better than stuff like the fourth chapter. Why isn't it in the single player game?" as well as "This doesn't even fit, why are FBI agents on an Aztec spaceship?" --- Help is a gift that one must never grow to expect. -- Willow (Witches' Brew by Terry Brooks)
Why did they suddenly appear in an enclosed lab area or boxed in street out of nowhere with a bunch of weapons lying around, and start shooting eachother? Multiplayer never makes sense. It's not supposed to.
Also, I wouldn't mind if the textures were lower grade/simpler in the "unique" areas. Hell, even Metroid Hunters had a bunch of "we never used this outside of multiplayer" maps, as well as every decent sized room from the single player outfitted brilliantly into a fantastic multiplayer arena. There's really no harm in making some basic textures, applying a few properties to one or two, and making a mediocre looking but deadly fun cathedral in the middle of nowhere for people to blow eachother to bits in. --- 2% of GameFAQs users have this in their signature. If you're one of the 98% that doesn't, copy and paste this into your signature.