"Canon" just means "this is the officially recognized record." Doesn't say a thing about how consistent it is. Making it all make sense is for dopes like us with too much free time on our hands.
As far as how much credence to give to TOS-R, well, Bob Justman saw at least some of the newly polished episodes before his passing and gave it his unqualified blessing, going so far as to say that this is what the original show should've looked like (so much for creator's intent being embodied by TOS Unexpurgated).
As for how the Concordance is gonna handle it, my money is on TOS-R being the preferred version, but that's just my hired-hand opinion, easily overruled. I also expected the new movie to be included, but I was surprised (albeit happily) by how that one turned out.