limud comes before covod cannot be applied so broadly, certainly not to a Godol removing his pants before a rabbim. do you think a Godol would teach while sitting on a Sefer Torah to make some point of limud?
If needed, Yes. No less than Avraham Avinu told Eliezer to place his hand on his Makom Milah, since it was needed. (Just thought of that off hand as an example, don’t ask me specific questions)
I don’t feel you need to follow his Mehalech (I’m not of that camp), so don’t feel it is required. I imagine many Roshei Yeshiva would never think to do such a thing.