Yeah to be fair the old Background was happy to admit the Warhammer World was a planet in the 40k universe however when 40k took off as well as it did they decided to seperate them into their own universes to avoid just such story complications.
Sigmar has become the Fantasy representation of the Emperor rather than a Primarch though it was hinted as you said. Who the other one was has always been debated though.
AS they seperated that idea was thrown out, though always hung around and the extra chapters were said to be placeholders for your own created chapters, to encourage people to get creative and imaginitive with back stories for their forces. There's 2 of these to allow 1 loyalist and 1 chaos.