OK, there is absolutely no difference in what is in the Gapps. It all has to do with where they go.
We have very limited space on our system partition, regular Gapps gets installed to system, while symlinked gets installed to data.
All apps installed by you go to data, while system never changes, just what is in the ROM zip, all settings and add ons go to cache, and data.
If there is not enough space on system, and you try to install Gapps, it will not give you an error, it will just finish like normal. After about 50 tests, the missing file was random. One time would be play not there, then maps would crash but play would work.
Any way, your better off with the symlinked for CM9 or CM10 on our phone. GNow doesn't really have much to do with it, it is just possible now to get a good install without running out of space.
Hope this clarifies things.