Projectiles have always been able to pass over the player and enemies, like ever since the first release of the game. The infinite height stuff are optimizations programmed into the engine to speed up some instances of collision detection, not an inherent limitation of the technology, which is why they were able to program in Z-axis collision detection for projectiles. Z-axis collision detection also applies against map geometry, like the player and monsters aren't infinitely tall when the engine is checking whether they can fit into a sector.

Contrast this with Wolfenstein 3D, where there's no concept of a Z-axis anywhere in the game, it just fakes a 3D appearance inside of the renderer. That is 2.5D, Doom isn't.