This also implies they never ran a simulation on the actual mission timeline (with the 11 hour delay between initial rocket startup and launch), or the error would have occurred during the sim.

Boeing didn't provide any information on their ground displays for this particular clock, meaning that ground didn't have any way of verifying this with a checklist. It's a value that should have been properly telemetered and displayed, but was not. Don't knock JSC mission control, they're extremely professional and don't make silly mistakes like that.

But what's crazy is that once the capsule disconnects from the second stage of Atlas, the only remaining part of the whole system... is the Starliner. So what other clock could they be looking at? The Atlas V blows up in the ocean.

Eh, there is no handshake for something like a clock reading from another system?

It was actually a layered failure. The "handshake" couldn't happen because the comm was temporarily disrupted due to the location in orbit