Solved easily enough by having a second patch and using the load order profiles. Thing is though, SotD has more than just story conflicts as I recall. I'm pretty sure it modifies Cloud Ruler as well as a few other places involved with RST.
SotD doesn't directly touch CRT as far as I know. It only places some NPCs but they're only enabled when reaching certain stages in the SotD main quest. One I won't be playing anyways. As for other edits... mhm Kvatch gate area, Blankenmarch (again activated by quest stages), some dungeon southeast of Leyawiin, Fort Oldanwor which is next to the KOTN priory, Ipsumali West of Chorrol and some small temple far up in the jerall mountains. For an old mod SotD is rather friendly in terms of compatibility.
If I run into any serious issues I will disable SotD and rebuild my patch, but if there really isn't any reason to do so, then meh
I never thought of using a second patch by the way, that's a good idea Arthmoor, thank you for that. Will most certainly come in handy!