I think the issue here is that while Thunderholme had never had an "official" dungeon representation (there was a short section on its history back in a 1998 sourcebook on the Cult of the Dragon), and therefore SSG had free reign to come up with their own interpretation, Temple of Elemental Evil is an adaptation of a very popular classic dungeon, and therefore, at least when it was created, taking any liberties with the material they were adapting would lead to a lot of complaining. (As it was a few diehard fans still complained that SSG had left the village of Hommlet out, even though that section of the adventure is basically just an extended quest hook with one or two fights with generic bandits thrown in and would have added months to the pack's development time.)
There are similar issues with the Against the Slave Lords chain, like the section in the second quest with all the fake traps that just feels weird given that the trick simply doesn't work in a visual medium. (Especially not the stuffed bear on rails, with a clearly human voice saying the word "roar" on repeat every two seconds.)
As time has gone on the quest design team have got noticeably more confident in making adjustments to the source material when it suits the game (best evidenced, I think, by Saltmarsh and Isle of Dread, which mix officially written dungeons with SSG-designed locations and pull it off pretty well.)
