That's bizarre! Quake clone / Quake killer was arguably a more famous term, and more widely used than Doom clone as Quake created & defined the first major professional online leagues, CAL, OGL, Quakecon, etc.
Quake set the standard, and it wasn't just the polygon advantage over build engine games like Duke Nukem 3D. It was the highly realized, competitive, free look multiplayer environment that shaped MP games even to where we're at in 2018.
So even in 1999 they weren't really just called FPS games, most everything was cross-compared to what it was emulating before it. You also get CS clones, CS killers that came later too. Same with Halo / Goldeneye on consoles.