Yes, that's the intention. Just haven't gotten around to arranging for these files to be accepted at the online portal yet.
Putting it into terrasync is a bad idea... different ppl have different data... you'd screw stuff up big time...
As far as I know it should not be a problem, because the Level-D parser will search first for the standard runway number, and then search for an override file if it doesn't find the standard runway number.
But honestly I'd rather update the apt.dat... even if there are some mismatches right now... this should all work well once ws3 with runtime generated airports works...
I don't agree with modifying the apt.dat file in FGData -- in general, modifying things in /data/ folder are to be avoided as a best practice. Any changes should be done either through the Scenery/NavData/apt/ mechanism for small patches, or else the entire file should be replaced by new X-Plane data from the Gateway. That would likely also involves updating navaid positions and 3D models.