I love your approach to set designs. Season 3 had a lot of different sets built, too:
The chapel set had three rows in Season 3, The Tholian Web #64. The chapel, set up for TTW, was probably reused for TDOD #66 (with the pulpit removed to un-seal the normal door to the curved corridor). Season 3 TDOD, the crew lounge was the briefing/rec room with an additional door to the straight corridor across from the transporter room, but it still kept the old door to the curve side, too.
I think the herbarium/rec. room (Season 3 ATCSL #60) was also the briefing/rec. room highly modified, or it may have been stand alone like the auxiliary control room. The room was the deleted scene rec. room built previously for Elaan of Troyius #57.