I've always thought of Doom re-implementations (in the TASing context; obviously there are enhancements for modders) as incredibly sophisticated tools rather than as emulators, though that's just a semantic distinction. Consider
the TTYD plane flight optimiser: it only covers 1 of the game's mechanics, whereas something like GZDoom covers every part of Doom, but in my mind they're analogous.
If you take Prince of Persia for the Apple ][, then unless you have a virtual machine interpreting or otherwise translating 6502 instructions into host machine code, I wouldn't consider that emulation.
So while I'm sure engine re-implementations would be useful for TASers, and can't think of a reason not to include them in BizHawk apart from bloat, I'm of the opinion that movies which only sync in them shouldn't be accepted. A movie ought to sync in a reasonably-accurate emulator for the relevant system, or better yet, on extant hardware.