1. Don't apply Character styles manually via Character Styles Panel, do it via nested styles or GREP styles. These are not automatically transfered to the TOC.
2. ?? I don't understand your question.
If I understand the discussion of nested styles correctly this ALMOST works. I just need to invent a (hidden?) character with which to end the nested style. Reason: I’m working with a bunch or orchidologists who have very specific ideas on styling, and what/where any marks occur in the naming sequence of their prized objects. IOW, my nested style has to end without any visible characters.
Wondering if I can end the nested style with, say, a comma, which is then ignored or formatted as hidden?
Looks like I finessed/dodged this issue, at least in this instance, by some sleight-of-hand with manual formatting. Will spare you the details unless they interest you for other reasons.
But if the hidden-character solution is feasible, that might be of future interest anyway.
Type > Insert special Character > Other > End of nested style. (I hope I have translated it correctly into English from the German version)