oh right i thought you meat you were going to expand an already existing territ_main.
In that case - no. the original protections won't be converted, they may remain but wouldn't be part of the city itself.
As such you'd have a hard time allowing perms as you'd likely have to add the player to the territ_main AND the original protection, which would mean sid player had unrestricted access to city, thus defeating the point of McTowns.
I estimate you could, with a mod paying attention/to guide, should you be unfamiliar with the workings of McTowns, convert it all to mctowns compatible in about an hour, assuming a largish city.