[OnePlus 3T Questions & Answers] mobilityguy:
Problem solved. The more I looked at the symptoms, the more I realized that the OTA I took after unrooting with SuperSU corrupted the system partition somehow. The first time I tried applying the OTA with the stock recovery it failed, but I was able to reboot and apply 4.1.6. That's when the trouble began - I was unable to reapply SuperSU. Fortunately I had done a nandroid backup between the upgrade and the attempt to re-root, and after the SuperSU script failed I was able to restore the backup (made and restored using TWRP 3.0.4-1) and continue working. It was either at that point or earlier, during the OTA itself, that /system was damaged - not badly enough to prevent the phone from working perfectly well, but enough to keep TWRP from mounting /system read/write. From that point on I was doomed. None of my other attempts to fix the problem had a chance as long as TWRP was restricted to mounting /system read-only. Then it got worse.

After a semi-failed attempt to install Magisk (rooted applications worked as long as they didn't try writing to /system) I restored my pre-root 4.1.6 backup one more time. After that, TWRP wouldn't mount /system at all, which prevented me from making any more nandroid backups.

It was time to act. I could keep using the phone unrooted, but the longer I went on the more work would be required to put things completely right. The risk would increase because I couldn't take any more snapshots of the phone to fall back to if I munged the device again. I also had a positive reason to fix things - during the two days the phone was rooted but couldn't access /system, Titanium Backup kicked in and did a full backup of all my software and settings.

With a damaged file system and full backups, there was no reason for halfway measures. I copied all my user data off the phone and used LloydSmallwood's unbrick tool to flash the phone back to its original OOS 3.5.4 state. That took care of rebuilding all file structures. As soon as I rebooted, OOS upgraded to 4.1.6 in one step, taking care of the system upgrade. Unlocked the bootloader, installed TWRP 3.1.1-0 (not 3.1.1-2, which has a serious bug for the 3T as someone posted above). I was able to mount and unmount /system from TWRP's mount screen, no problem. Ran Magisk 13.3 script without a problem, installed Titanium Backup, and tested an app restore. No problem. I'm now in the midst of copying all my stuff back onto the phone, after which I'll restore all missing apps and be back in business (I hope).

It's possible I could have done something tricky like reformatting /system and restoring the partition from my last good nandroid backup. But I always would have been concerned that problems would have popped up later, maybe during the Android O upgrade, when it would be way too late to recover my then-current setup. After seeing virtually every combination of working and non-working features, it just made sense to build from a clean system.

So thanks have been given to LloydSmallwood for his absolutely indispensable unbrick tool (this is the second time it has saved my phone). I should also thank my Galaxy S3, running the current build of LineageOS, which has gotten me through the two days it took to set my OnePlus straight. The Galaxy has performed better than a five year old phone running brand-new software should ever be expected to - if it supported LTE I could consider using it as a daily driver. This has been an education, and a reminder of how important it is to keep good backups at every step throughout an upgrade - and routinely during production use.

Thanks to all who gave advice in this thread.