This is a huge argument that streches from before the Trojan War until present day. Plus, many people have strong emotions and are quite invested in it.

Simply put, Macedonians weren't nessicarily the same exact people as "the Greeks". "The Greeks" would often think that they were inferior and didn't like them due to their dialect (which Philip switched to Attic Greek anyways, so their language differences were not an issue in our time period), culture, and different traditions. Of course, you have to keep in mind that "the Greeks" thought less of everyone: the Persians, the Egyptians, the Etruscans, even other Greek cities when they felt like it.

The Makedonians were probably the same race of people, though not "pure" like the Southern Greeks due to their proximity to other peoples.

Even though, it may be argued now that they are the same people, at the time they didn't nessicarily think so. The southern Greeks didn't like the Makedonian (or the even Thessalians all that much, for that matter) and there was some discrimination. And the Makedonians returned that disdane.

And remember people, names, racial locations, and likes & dislikes of today don't have nessicarily anything to do with people, names, racial locations, and likes & dislikes of the game's time.