Turns out I was wrong, it's built from the ground up (with a preexisting engine) and uses the ROM for certain data like music and sprites. I guess DOOM 64 hasn't actually been hacked and the code is still a mystery.
Man is it fun to play this game with mouselook and jumping. It really breaks the game design in places, like in level 2 where instead of going throughout the whole level to get a yellow key card which opens the exit door at the beginning of the stage, you can just hop the ledge and go straight to the exit, lol. But it's still a fun way to play, you just gotta limit yourself a bit if you wanna play somewhat as intended.
It's also great to have WASD controls. The N64 game had this weird control scheme where the joystick moved the player forward/backward and looked left/right, and there was no C-button option for forward and backward movement, only strafing, so it was a weird hybrid of sorts. On the N64, I always preferred Turok controls, which used the C-buttons for movement and the stick for looking.
The only bad thing about Doom64 EX is all the bugs causing it to crash. The developer updated it as recently as February, so he's still working on it. (Initial build came out in 2009 or something.) Hopefully he irons out the problems, but currently he's obsessed with doing his own PC version of Turok: Dinosaur Hunter, and has intentions to port Blood using the engine he did DOOM 64 on.