score:3
I figured I'd answer my own question in case anyone else has this issue. As I mentioned in a comment, the agency that issued my invitation said to leave off the Trans-Sib from the hotels section. I did include it as a "city" to visit, however. I just got my passport back today with the visa in it, so I can confirm that is the correct way to do it.
Upvote:2
OP comment provided the answer:
I managed to get ahold of the agency that issued my tourist invitation. They said to leave the Trans-Sib off the hotels section entirely.