It's because of the particular things each system was best at, and could better accelerate. 3D games were actually one of the few cases (plus a few other number-crunching sims?) where games ran faster (not just "at the same speed") on the ST rather than the Amiga. And it's entirely because of the reason you first posit; the Atari had an ~11% faster CPU clock.
The games in question were very heavily CPU-bound, their simulation, and their drawing as well, relied almost entirely upon numeric calculation (and getting stuff in and out of RAM, which was also faster). The actual moving-data-to-the-screenbuffer part was a relatively small piece of the whole setup; I daresay that the Amiga's custom chipset still made that operation somewhat faster than the same job in the ST, at least what parts of the job it was actually capable of accelerating (it's not really much of a GPU; it's pretty much just a console style hardware-sprite-and-scroll engine, with a few fancy tricks like line-by-line auto-fill which helps a bit with rendering solid polygons if the programmer knows how to / can be bothered making use of it, or the register bit-banging provided by the Copper), but the ST was already entirely capable of shoving the calculated and rendered output to the screen pretty much as fast as it was produced (by double buffering, so the final "painting" of the screen was a single register-write), so the best it could have done was maybe shave one scan-time off the construction and display of each frame.
There's no line or box or other primitive drawing acceleration, no large-area auto fill, no bezier curves, absolutely nothing that would count as even the most rudimentary 3D acceleration, the sprites or second playfield only appear as overlays (and for the most part are irrelevant here, other than PF2 being used as a cockpit/HUD for a fairly minor speedup), hardware scrolling is pretty much useless, as are most Copper tricks, and even the (less efficient than the ST's - assuming the Atari had one fitted of course) Blitter is of limited usefulness.
If the complexity of the scene was such that it took the Amiga CPU fully 8 scans to finish computing and rendering the image, but the ST only needed 7 (entirely plausible given that a lot of 3D polygon games really struggled to do any better than maybe 6~7fps, which is a 7 to 8 "frameskip" on a PAL monitor, and worse on NTSC), then even that minor improvement to the rest of the system latency wouldn't do anything more than bring them back to level-pegging.
Pretty much any other type of contemporary game, sure, the Amiga had it comfortably in the bag. But for sims and other 3D stuff, the ST just about nosed ahead.