My buffer is at 1024, and that's the amount that the recordings are late in the timeline. You can see the highlighted selection in the transport.
Every interface reports its buffer latency to the DAW via its driver, and the DAW places recordings into the timeline correctly per that amount, regardless of buffer setting. This normally works perfectly in Pro Tools, and now it doesn't. To be sure it wasn't a firmware error in the Apollo, I did the same test in Logic Pro - it was spot-on:
