I'd say the biggest thing is that SW has proven before they have no issue with using bits of extended universe and completely ignoring others. Example, Chiss being involved with the sith at this point in history, Rakata being involved at all, Sith purebloods existing in this time period etc etc. Bioware is infamous for taking things it likes, and ignoring others, just like LucasArts.
I'm not gonna discount the emperor being Abeloth. I wouldn't also believe anything regarding the emperor's indentity unless it's a confirmed legit Lucas Arts/Disney or Bioware resource. Not extended universe.
Well it's not Abeloth so we don't really have to worry here. His identity has already been confirmed. :P Oh and too my knowledge BioWare created the Rakata race so they can do whatever they want with it. And I see no reason why pureblood and chiss cant exist at this time.
But really though, it's not Abeloth. BW aren't going piggy back post ROTJ lore that is probably going to become noncanon when the new films are released.