Yes it was amazing how the Grim Sleeper was caught. Imagine the astonishment of the detectives when those results started piling up.
With Bob's case, there is primary DNA on file. As far as I am aware, there is no other DNA from the family that has been entered into CODIS. All of the skeletal remains that pop up all over San Bernadino county have to have their DNA extracted, and that process can take a while because of the backlog at UNTCHI. Unless, of course, CA chooses to process it themselves. Because they have their own DNA database, like some other states. I am pretty certain the databases link up with CODIS....in any case, sample to sample comparison can be done fairly easily if you have samples that you can compare...like a toothbrush from Bob and a molar from a John Doe.
There are other means of identification-dental records are pretty rock solid and even radiographs/xrays if DNA or dentals arent available.
I was helping out a family once-we were trying to compare the Missing Person to some (unfortunately) disarticulated remains. We had no dentals and this was one of the families who was incredibly reluctant to give DNA. The Missing Person had been in a car accident several years before and she had a head CT and an XRAY of her jaw at a hospital. The ME was able to use those two items to rule out a match to the Jane Doe.
I have had situations where creative and hardworking LE contact Quantico to have them compare photographs of (for example) a missing child to a set of remains. They do layovers.
Oh and one more option/story-I had a group contact me once to test some facial recognition software they were working on. They wanted to take the information from a John Doe and run the image through the software and compare it to DL's on file for all of the states that were online.
My point is that there is always a way to do identification outside of NAMUS-but it would be WAY easier if everyone used NAMUS and FRS were available in all cases.