After a quick scan of the General Handbook, I found 29.2.1.1 (item 3) pertaining to Sacrament Meetings:
"Presiding authorities and visiting high councilors should be invited to sit on the stand. General Officers are also invited to sit on the stand unless they are attending their home ward."
So at least for the Ward organization, presiding authorities are invited to sit on the stand [at the front of the congregation] during Sacrament Meeting.
I didn't see it immediately noted in the handbook/didn't search, but it's likely the same protocol for Stake Conference or other large meetings of Saints (Area Conference, General Conference, etc.)
Whether the seating policy has changed over time is an interesting question. As far as I can remember, the Stake President and his councilors have always sat side-by-side at the head of high council table; and back (eons ago) when I was a child in primary, the Primary presidency always sat at the front of the room -- but other than that, in my Deacon/Teacher/Priest/EQ experience, seating is most often a semi-circle with leaders sitting wherever (though, as expected, they will stand at the forefront when making announcements, teaching, etc...)
Usual disclaimer: I'm not an authority/expert on church policy
