Why does Setite Sorcery include multiple, separate branches of blood magic?

[AnubisXy]

There is no basis. Glory to Set.

*diablerizes you*

I'm not sure where you're getting your ideas from. The witches are a thinly veiled lilith cult. Meanwhile the FoS have overwhelmingly been fast and loose when it comes to Set and they've been very happy about it. Thor? Set. Zeus? Set. Indra? Set. Nidhogg? Apep. Buddha? Set. Mara? Also Set. Yellow Dragon? Caine? Set. Eden serpent? Also Set. Mythical Snakes and Horny Storm Gods are a dime a dozen. The reactionary element of the clan who've been all -Egyptian Set and Egyptian set alone- have always been a small minority within the cult and even then it's difficult to say how many of them believe you shouldn't use masks at all and how many of them believe you can dress up Set as much as you want so long as you acknowledge the "Egyptian Truth".

V20 Book of Secrets, the section on the Witches of Echidna. It notes that they believe the various off-shoots of the Followers of Set (the Datiya of India, the Children of Judas, the Hall of Jormungandar, etc) aren't following the same deity but are following different deities. They also believe that Set/Typhon are dangerous and have something dark planned for the clan.

Each of these lines — and more — practice Setite
Sorcery in divergent ways, calling on different benefactors
and applying the results in varying terrible fashions. The
Witches of Echidna seek this conclusion. They recognize
the perfidy of Typhon, and his will via the actions of Setites
pitched against them. While they fight against their fates,
they zealously attempt to spread the blood magic cultivated
over millennia, to ensure their clan — in whatever form it
takes — remains strong against the slaves of the Aeons and
the caprice of their Antediluvian.

Setites differ wildly, and while many possess zealous piety,
this allegiance is to as many gods as there are cultures. Akhu’s
practitioners tap into and subvert the power of vampiric faith.
Faith spawns devotion; devotion leads to blind fanaticism; fanaticism
leads to chaos. Cainite scholars who study the Discipline
describe it as the power to forge chaos into a tool — whether
that tool is for aggression, seduction, or transfiguration. This
blood magic is a tangled weave of ethos and dogma, with each
cult of practitioners declaring dominance over its peers.

Followers of Set who know of their sorcerers identify them
as a peculiar breed. While divergent faiths rarely see eye-toeye,
the Witches counsel the different creeds on sharing a
sympathetic relationship. Each one believes he or she is correct,
so while they may undertake varied journeys, damning one
another for heresy is in opposition to their respective dogmas.
Their acts of sacrifice and supplication to the gods at whose
feet they kneel unify them, in a mutual, terrible aim:
Their sorcery will strengthen the clan. Their sorcery will
identify their founder’s location. Their sorcery will please
their founder and make him love them forever. If this aim
is not accomplished, their maddened founder will be sure
to consume them.

- V20 Book of Secrets 60-61

V20 Book of Secrets sets the line that different sects of Setites worship different gods, and not all of them believe that those are simply masks of Set. The Witches seem to hold that all of these beliefs are correct at the same time and they support those very heretical beliefs. It's why they ultimately get wiped out as heretics by the main-line, orthodox Setites. But it seems like their beliefs managed to survive them because the V5 Ministry, which worships numerous gods, seems pretty similar to what the Witches were espousing.

White Wolf was bought by Paradox in 2015. Book of Secrets was published in 2016. and V5 was published in 2018. It's possible that the Setites/Ministry split was decided and the segment on the Witches was included to pave the way for that split. Or it's possible that someone saw what was published with the Witches and decided to use that as the basis for the Ministry.

Whatever the case it feels like the Witches of Echidna were the prototype, inspiration or laid the groundwork for the Followers/Ministry split that we see in V5. Then from an in-character perspective, the Witches knew that their time was numbered so they gathered up magical knowledge and spread that throughout the clan, along with their heretical beliefs, hoping/believing that someday it would create a scism within the clan. We do see a scism in V5 so it seems like the Witches heretical beliefs won out, it just took almost a thousand years for that to happen.