They can compare the known autosomal markers, as well. However, in this case, if they found semen (which is a fluid that contains DNA and has its own proteins that are discernible for some time after death). I don't think that was any sort of rushing creek, so it's hard to estimate how much was left - but clearly, it was a man - if they can find DNA, they certainly can find larger molecules.
So...the Y chromosome doesn't contain a whole lot of markers that are individual - it only confirms he's male (and a few other rare traits could be there - for CODIS to look at).
But they have DNA from the two women, so they can exclude that from their study and piece together the fragments they have of autosomal DNA (the other 44 chromosomes + the man's X chromosome - so 45 other chromosomes with thousands of genes). Some slots in the genome are highly variable and they look at those in CODIS - and that's where a possible match begins.
It's never a slam dunk, but I hope fervently that some of it will be useful. CODIS doesn't generate profiles - and to do that requires an entirely different kind of study. Use of DNA based profiles is still very young - but I think the main point of it is to ID someone already in the system. I also believe that this particular criminal has been in the system - has been caught before.
If he hasn't, then yeah, it's going to take several different types of expertise to get any kind of profile.