If you want an example of something that’s really an unsupported use case, consider mid-frame palette changes—in order to do this, you actually have to disable and re-enable rasterization during the horizontal blanking interval. It works, but it is difficult to get right and the PPU is clearly not designed with this in mind.

Short of having an actual spec in hand, it would appear that mid-frame scroll register updates were entirely normal and an intended way to use the device, based on the evidence (no other reason for sprite zero check, lots of first-party titles using this feature, other mid-frame updates are much more difficult).