Ok, so we're essentially agreeing in a roundabout way. I just didn't understand from your prior post, thinking you were saying that you'd be able to take OTAs without worrying about losing Root.
So in other words, so we're clear, I'm assuming that taking an OTA once rooted, even if you do so with HTC's bootloader unlock method, will likely result in losing root (based on current knowledge).
My current knowledge of how future OTA updates will work is non-existent
I'm basically thinking like an HTC engineer: if I have a ton of devices out there with potentially unknown configurations, how can I guarantee that my update script will succeed? I see two likely scenarios:
1) blow away everything and start from scratch
2) require a stock kernel and system before the update will work
The main problem with option 1 is that it means you have to kill the user's data, especially if the user is using an AOSP ROM. Replacing /system but not /data would cause some serious corruption in that scenario. Current OTAs are fairly seamless, meaning the update happens around the user's apps, data, and settings. I'd imagine this will remain a priority.
Option 2 seems more reasonable. The OTA update would check to see if the phone's contents are fit for upgrade. If not, it refuses to install. Which means that if the user really wants the OTA, s/he will have to bring the system back to stock. I would think a rooted stock ROM would suffice, although it would likely have to be odexed. su may or may not be preserved, but if it's enough to coax the OTA to install, the user could add su back.
But my main point is that whatever HTC decides to do with OTA updates, it should be irrelevant to users who are fully rooted, either by official or unofficial S-OFF. Rooted users should get into the mindset of flashing their updates, not accepting them over-the-air.