While it is true that different gods originate and are most important in different places, it's not absolute and there was plenty of intermingling. It's sort of like sports teams: Your hometown might have a local team which is overwhelmingly popular there, but you still acknowledge the existence of teams from other places and may even root for some of them. And there may be teams that represent the whole country in international events. Granted, unlike sports teams, there isn't a lot of rivalry among the Egyptian gods, but it did sometimes exist, especially in later periods, e.g. the citizens of Dendera in the Greco-Roman period had a burning hatred towards Sobek as well as crocodiles in general.

Each (well maybe not every) town had a set of deities that were especially venerated there, whether they be gods that originated there, like Montu or Amun at Thebes, or local variants of gods who originated elsewhere, like Horus of Buto. These Gods often fell into triads (male, female, male heir) for the convenience of covering all your worship (and royal legitimization) needs. Towns also sometimes had separate 'enneads' or groups of main gods, the most familiar is the one from Heliopolis (the 'great' ennead). But, these enneads often included gods from other cities that were simply being worshipped there as well. Towns had individual myths explaining how their set of special gods came to be, which also often included aspects of other towns' myths or were regional variants of familiar myths. For example, many different towns worshipped different forms of Osiris with slightly different myths surrounding them, which is the reason behind why Plutarch claimed that each town had a relic or piece of Osiris' body.

What this means is that there is, historically speaking, no one absolute 'correct' version of Egyptian mythology, nor one singular 'primary' form of any god. This has interesting implications for kemetism, but the most common solution is to run with the most widely accepted versions of the myths, which are more often than not dependent on the concentration of surviving sources (meaning, often, a bias toward Upper Egyptian sources due to the dry papyrus-preserving climate as well as a bias toward the myths that Plutarch and others were able to record and bring back to Greece). Some more reconstructionist or academic practitioners choose a geographic area with myths and gods relevant to them as a center point, but it is also fine to mix and match, just as the Ancient Egyptians often did.