I just checked q3map2 source code for the "-patchmeta" option for when it considers two patches to be part of the same LOD group: it assumes they're together when they have a vertex that's - in X, Y and Z - less than 1 qu away from the other (not absolutely equal, like your code requires).
Maybe you should do the same in your code. Sometimes mappers simply don't manage to get the vertices ENTIRELY on top of each other, e.g. if the patch has been affected by a scale or rotate operation in radiant.
As for the tesselation:
Currently, at tolerance 4 (default), a bestsquareddeviation of 16 or higher is needed to get 1.0 tesselation. I simply think that the specific patch gets a lower deviation there. Maybe the 1/2 "tesselation" should simply be entirely avoided unless the patch is REALLY mostly planar (i.e. in your bestsquareddeviation < 0.01f case)?