I think these are all the settings. Maybe see if anything is different between the two projects. Perhaps PDF/A or 'export layers' is affecting things.
I had compared this previously. Both are set identically, as far as I can tell. (To archive PDF/A-2a, no layers) I just tried publishing the entire set again and get the same result: one plan generates bookmarks, and the other doesn't.
EDIT: I think I found the reason. I finally noticed a bunch of scratch files for the non-bookmarked version. So I opened the file with "Open and Repair". No more scratch files, and - VOILÀ - Bookmarks!
Hope this helps somebody...
Richard Morrison, Architect-Interior Designer
AC25 (since AC6.0), Win10