In case it's helpful, here's a screenshot from TES4EDIT showing the interaction between Knights, RST 1.05, LMR, and the LMR-Knights patch around the default altar.
When looking at things in game, it looks like the Altar of Arkay added by LMR and the Altar of the Nine added by RST are overlapping each other, as their coordinates are identical. That may or may not be a problem, since depending on where the mouse is on the altar you can select either the Altar of the Nine or the Altar of Arkay object to activate it. Given that, I just don't have enough of an understanding about how RST is supposed to work to know whether things will work as they should at the appropriate times, so I appreciate the support you guys are offering.