Do the red and green Fossoways count as two different Houses?

Yes. The red Fossoways belong to the lordly House Fossoway of Cider Hall. Their sigil is a red apple on a field of gold, and their words are “A Taste of Glory.” 

The green Fossoways, by contrast, belong to the knightly House Fossoway of New Barrel. Their sigil is a green apple on a field of gold, and their words do not appear in the text. 

So: different sigils, different holdfasts, different statuses = different Houses.