Not sure exactly how the N64 version works, but the PC version uses a lot of engine tricks to make the levels. Much like Doom, the Build engine doesn't support true room-over-room*. For example, on that first map, when you drop down the air duct, your are seamlessly teleported to another part of the level. There's also some usage of sprites to make 3d platforms.
While the game isn't a complete port, I doubt they re-wrote the engine from scratch, so you'd probably run into some weird things.
On a side note, the Build engine was really fun to make maps with. Even though it still wasn't true 3d, you could make a lot of cool things. I'd actually be interested to see if it would be possible to extract scale coordinates from the N64 maps so you could possibly make PC versions out of them. Since they had to take all of the adult content out, they ended up re-doing some of the levels, and IIRC there are some originals.
*However, unlike Doom, Build allows for rooms to overlap on the X/Y axis, as long as there is no intersection on the Z axis, and neither of the rooms share any veritices.
