Thank you! ^^ I've been a bit slow, but I do plan to keep at it.
Tested more values and found that $C5, $C7, $C9, and $CE all also result in the ending skip, once again in the same conditions. It seems that only invalid trashcan objects will lead to this particular skip -- and somehow, fairly consistently. I tested all spell values as well, with nothing of note -- updated the gist from earlier with details.
Also, the new skip values have been put to good use, and I have a new movie 185 frames faster than the previous. fm2 can be found here:
http://dehacked.2y.net/microstorage.php/info/1589758643/zekna_randil_shadowgate_v5.fm2
The old lab setup and route to the acid fountain are abandoned in favor of raising the bucket in the courtyard to make $DD in $04E4, which is used to skip to the end.
As a side note, I have been using the tas editor/fm3 format to make this. They've been a pain to upload through the usual means, so I've been exporting to fm2. If anyone wants the actual fm3 file please let me know! I'm happy to provide it, and intend to submit using fm3.
And, as always, please take a look. Any feedback is very welcome.