I wrote both of those sections and not only are they not incompatible with what I have written in RQG, but I wrote them with the goal of getting to this point. Greg and I talked at length about the treatment of Yelmalio in RuneQuest and I know he was fine with it.
For the purposes of RuneQuest, Elmal can (and will) be treated as a local variant of Yelmalio. Same thing with the elf variant of Yelmalio and the Pentan variant of Yelmalio. A worshiper of Elmal can go to a Sun Dome Temple and contact his god (i.e., replenish his Rune Points). A worshiper of Yelmalio can go to the temple at Runegate and contact his god (i.e. replenish his Rune Points). To make things more confusing, Elmal is often a title of Yelmalio, and Yelmalio is often a title of Elmal. The Elmal variant says Yelm is the father of Elmal, but sometimes calls the Sun Disk Elmal and sometimes calls the Sun Disk Yelm. The Yelmalio cult does the same. <As an aside, the Yelm cult never calls the Sun Disk Elmal or Yelmalio and can draw much more substantive powers from the Fiery Sun than any of the Yelmalio variants (who only get Sunspear through the Yelm cult).>
That's the similarities. There are some magical differences between the variants. The Yelmalio cult takes on all sorts of strange geases to get gifts from the god, the Elmal does not. Elmal is associated with Orlanth and not with Yelm. Yelmalio is associated with Yelm and not Orlanth.
In play I don't think it doesn't make much difference. If someone from Sartar wants to play a solar worshiper they can. Their choice is basically establishmentarian (Elmal) or dissenter (Yelmalio). Mechanically the only differences are associate cults (Yelm or Orlanth) that the Yelmalio worshiper gets gifts and geases and fights with pike and shield, and the Elmal worshiper does not. Socially the Elmal character can insist that the Yelmalio worshiper is "doing it wrong" or "taking it too far", and the Yelmalio character can insist that the Elmal worshiper "values tradition over the gods" or "values tribe over the truth" - but as far as the rules are concerned, they are worshiping variations of the same god. Same thing happens when an Tolat worshiper from Melib comes to Alkoth and meets the Shargash cult (Tolat and Shargash are presented as variations of the same god).