I always slap an Edit Mesh modifier below my projection cage before handing off to xNormal, and keep it for exporting meshes to engine. That way triangulation should stay consistent. d'oh. is part of the problem their uv channel 0 lookups for specular lightmap calculation? so annoying.
Depending on the situation, I've had some luck getting cleaner normals by using TC_NormalmapUncompressed instead of TC_NormalMap. DXT compression is great for efficiency, but on something like a normal map, you need exact normal colors on those edges or you'll get a small seam. The tradeoff using Uncompressed is you gain…