I think I've asked this before, but how sure are we that there is such a thing as one god wearing multiple faces? Manathlaan and Mannan seen like the best test case, but I don't think we've ever gotten confirmation.
So I think we need to treat it as still an assumption, that just because two differently named gods look largely the same if you squint, they are the same god.
There's many examples of Gods being considered different names for the same being by a character in the story, some more plausible than others. Cython famously loves fitting human Gods to elf Gods, but we have indication that he probably went too far at least once - he's pretty sure that Kurnous and Taal are the same being, but the investigation of the Cult of Karnos gave pretty strong evidence that Taal and Kurnous are separate beings despite looking
very similar. I definitely agree with you that we shouldn't assume similar Gods are definitely the same being and I think the Cult of Karnos is something of a cautionary tale in that regard. Ljiljana talked about Ranald getting some Gods killed at Salyak's request, which probably implies a connection between Ranald and Salyak and the elf pantheon but even more likely implies that Salyak is Shallya, which is already a pretty common theory in and out of the story. Deathfang says Rhya
isn't Isha, but also identifies the energies of Ranald as the energies of Loec, and Mathilde got a sense of familiarity from looking at a picture of the Nehekharan God of subtlety and snakes, Qu'aph. So and so forth.
I would say that the most clear-cut example we got in the quest was Halétha, Haleth, and Kalita. Aksel straight up told us that the Cults of Haleth (there are two different Cults worshipping a Goddess by that name) were guises of Halétha, and that they rose up when worshippers of Halétha that were worshipping Her away from their native communities had to hide their worship to avoid persecution. We already suspected those Goddesses might be related because of their names, and our books on Minor Gods of the Empire confirm that the timeline fits Aksel's story (those Cults rose when the Cults of Taal and Rhya were gaining influence in the Forest of Shadows, and those Cults likely persecuted the Cult of Halétha). What was more of a revelation was Aksel telling us that the Kislevite God Kalita is a guise of Halétha, and gender aside this is very surprising because based on what we know of Halétha those Gods do not look very similar
at all. Kalita does kind of resemble Ranald the Dealer, so Mathilde sort of figured maybe that's the way to explain it.
Now if you really want to insist you can say that even that isn't confirmation, maybe Aksel is wrong, but Aksel isn't saying "those Gods look similar to my Goddess so clearly They are Her", he is saying "those Cults were founded by followers of my Goddess who were hiding their worship, this is a historical fact I'm aware of", so I really think we can take him at his word. The way to super-double-confirm this would be to talk to followers of Haleth or Kalita with the Father active and see if they trust us (but maybe that's not enough of a confirmation - what if
Ranald is lying and secretly making our coin
more useful than advertised???) which honestly is an additional OOC reason why I think we can trust Aksel here, it would be kind of a mean red herring if he was wrong.