I've been rolling this around in my head in regards to the bugs thing. I guess what I hear now is that south Freeside is the merged Freeside rather than North?
Is that because the worldspace of south Freeside doesn't fit inside the walls where it's "supposed" to be?
Since there's no way to get to South freeside without going through North it just seemed like the natural way to build a merged Freeside would be north to south. That's why the bugs were so confusing. They all appeared in the "main" (to my mind) Freeside. In this context of an expanded south Freeside becoming FreesideOpen the bugs mostly make sense.
That being said the problem with the TTW Freeside train station is a problem because the two buildings don't line up in the open freeside and it required no clipping to find working doors. I guess it's probably still straight forward as far as moving from one to the other but there's a lot more involved.