My perspective on Maya and Phoenix's relationship is different from my perspective on Phoenix and Edgeworth's... because those two relationships are different. Phoenix and Edgeworth interact in a completely different way from Phoenix and Maya, they have a different history, there are different nuances to the way both pairs of characters regard each other.

Given that, you're of course perfectly free to think of Phoenix and Edgeworth as good friends, too, if that's what you prefer.