I think the reason you see a modification in the brackets and braces section of Layout Options is because of a little bug in the new option for showing sub-brackets when a single staff of a divisi section is present (see here).
For the rehearsal marks font style, you’re right that probably Dorico shouldn’t even show it in the Library Manager any longer, though it does continue to exist in the project for the purposes of backwards compatibility, and it will be modified when the project is saved to match the current settings of the paragraph style, which explains why it is different in a project that has been saved and one that has not.