Thanks for the idea! I unlinked it via the Roku website and power cycled the Roku. It came up and all the channels were gone except: (Settings and Channel Store, plus HBO GO promotional channel) Netflix, Hulu Plus, Amazon Video, and very oddly, it also added MLB.TV to the channels, though I never had added it to my Roku Player at any time. They were even in the same order I had them in prior to unlinking my player (except MLB.TV which I never added). I opened up Netflix and Amazon as tests, and was able to browse my queue (Netflix) and library (Amazon) and play video from each, without being signed into the Roku player using a Roku account. Odd. So I tried the factory reset again from the Settings. Same exact thing after reboot. Still had my wireless password stored, same channels, still able to login and use them fine without having to re-set them up or re-link them. Then, I did a reset again, and this time I re-linked the Roku Player. Upon reboot, it downloaded 16 channels total, the ones I had previously, just like before. So I'm back at square one. Clearly, something is very amiss here.
One thing I did notice recently... which may or may not be responsible for this problem.
I had the Roku Holiday Channel added last year and never removed it. When I upgraded to a Roku XS 2 when they first came out some months ago, it automatically downloaded this channel and it still worked fine. It recently disappeared without me removing it. Every time I do an update or go into the Channels, it shows on screen that it's updating the Roku Holiday Channel. Every single time. I wonder if they didn't remove it and somehow it corrupted something in my account, or on my Roku, and there's no way to actually remove the channel via the player now, or via the website, so far as I can tell. I'm not sure if this is the cause but it is actually the main reason I wanted to do a factory reset in the first place, to get rid of the message about it that is frequently shown on the player's display.