My own personal theory:
The civilization of ancient Kemet spanned many centuries and was undoubtedly even more complex than our current knowledge of it suggests.
It would follow that many subcultures flourished, at least for a time. So there would have been no shortage of groups whose belief system was quite different from, if not in direct opposition to, the domonant paradigm of that era.
If one goes on the assumption that modern groups (such as the Kheprians for example,) are indeed viable and therefore connected to a spiritual lineage, then we have modern groups who choose to connect with facets of ancient Kemet that will probably never make it into print in any modern publication.
Then of course there are the many groups who go with an ancient Kemetic theme because it's so cool.

This response was brought to you by the miracle of little sleep and much caffeine.