On second thought, I've noticed your "Endless BG1" mod just now and I am mid-way reinstalling the game with it. Guess this playthrough goes down the grave
I have attempted to start new game in BG2:SoA and ToB for test purposes and Chapter enumeration seems to be alright here. Don't know how would BGT Worldmap be responsible for the issue indeed, makes sense to me, shall see once I reach BG2. If the issue continues, it's gonna be annoying for a purist like me, but I'll live, nothing gamebreaking it is.
As for SoD locations, I don't have any of them mentioned in any of the files installed (or haven't found them yet) so that might be the reason names are not displayed.
Unfortunately I am aware that map will remain in this current save and I know that reinstalling most likely won't help, oh well, might try once I finish this playthrough and find the time to try it again in the future.