GPOS based kerning can handle pairs and classes equally well. Kerning in the 'kern' table can only do pairs (ignoring Apple's extensions for AAT for the moment).
Most Adobe fonts have both pairs and class-based kerning in the GPOS table 'kern' feature. This works just fine.
If you are asking about having both GPOS kern feature and 'kern' table in the same font, that's another question. The results of doing so are undefined in the spec, and there's no guarantee what will happen. But a number of folks have done it, without obvious disasters occurring.
Regards,
T