How can I isolate what is causing the temporary "stall" during startup? As I see the progress bar on my MacBook Pro mid-2015 move from left to right, soon after it gets past the halfway point, it starts to slow down and eventually stops temporarily, at about the time the cursor appears. Then the spinning system cursor appears for about 3-5 seconds, and the boot sequence continues normally (and finishes).

How can I troubleshoot this? My wish would be to avoid a clean install and restore from scratch.

I previously reported the same problem under High Sierra.
I'm pretty sure it's disk encryption (FileVault2) that is causing the delay. I had to erase my internal flash drive and restore from backup. In so doing, I reformatted the flash drive as normal APFS and not APFS encrypted. There was no delay in booting. After I enabled FileVault encryption (and it finished), the boot delay returned.