My 2 cents you are over evaluating the issue.
Threads has a completely different structure than Classic.
PHP versus cgi.
MYSQL versus a flat file system.
Once you finish upgrading you will not deal with cgi anymore not above and or below the root locations.
You will have php scripts and all the data will be stored in MYSQL.
Probably the reason the import script did not work was because of your reported problem of the members folder above the root was not accessible so the script died trying to import posts because the poster list is in the Members directory.
Don't forget the importer is a php script not a cgi script.
I had a similar problem when I upgraded to threads. I had the member files above the root and I was on a windows host.
It sounds like you are on a dedicated or vps server and you have more control over your server than I had. But the most simplistic resolution for me was to move the members directory below the root set file/folder permissions update the control panel. Then run the importer for threads.
I don't understand what other directory's for Classic other than the Member files would have been above the root in your case. But I never had a need to do so either.
All you have for paths in the control panel is cgi files, Non cgi files,Variables files and Member files.
The directories can be named what ever you want but the setting paths remain as I stated above
So what other path setting are you talking about that is above the root other than member files?