The only monotonically increasing clock available on iOS is based on uptime. If you need to measure accurate timings or guarantee that events are in the right order, you have to use it. As Apple points out in their guidelines, there are many legitimate uses for this information.

Developers can add an offset to the values before sending them off the device, and that might be what Apple wants them to do, but these companies have over a decade of pre-existing code that didn't do this. It's not surprising to me that there are things that haven't been updated yet given that Apple only made these requirements public fairly recently.