if the aforementioned event occurs, you'll be going up against other super units.
not if you just buff the players unique units like the example u gave, Macedonian phalangite brigades, and the example i gave, companion cavalry, theres also Philips bodyguard, Hepatitus or something ;)
Well, for as long as Macedonian cities (ones that are far from the starting point, like Bisaltia or Mydgonia) are in enemy hands, they'll have access to those super phalangite units. Hypaspists is the other one you're looking for. Not quite sure how effective hepatitis would be as a weapon. :P
To avoid getting softer cities getting hit, build walls around most cities (if you can afford it) and garrison with one or two spearmen brigades. Otherwise, expand to strategic chokeholds (like the fort south of Heracleum, or Elimea, or the fort at Python, southwest of Metropolis, or Lamia.) in a region as quickly as possible. Personally, I use my cities as points in a defensive line that take advantage of geography, eventually dismantling the inner rings as your empire expands. This is slightly easier in the more mountainous west.
For example, after going south to Thessaly, take Tricca, Metropolis, the fort at Python, and Lamia, and all the cities in between, and also to the east down to Olizon. Everything any further inland than Pherae, Lamia, Metropolis, and Tricca can be relatively safe without walls so long as you hold those cities. You'll need to keep a few brigades around Pherae, because the Athenians like to land there sometimes, and you'll also want to make sure to hold the fort at Python. You may also want to take Tymphaia to the west of Eordaea and Elimea, because it provides a nice buffer area with mines.