I just did this last week and the check in counter agent knew exactly why I was doing the same day turnaround. The ISM was a bit surprised to see me on the TPE-HKG segment but got it when I told her why I'm doing it. I had c. 90 minutes between landing and taking off again.

FWIW, I checked in a bag when returning from NY. They checked it straight to HKG and then I told the lounge attendant that I am not planning on flying HKG - TPE and back. She just asked for my boarding passes and there were no issues.