Mo, The exception to peg holes before mortices is when using a boring machine and you are relying on the the feed screw on the boring machines bit to pull itself through the wood and it runs into the predrilled peg hole you then have to deal with that and it is a pain in the neck. So drill the mortice first, peg hole second.

As for speed, on a single mortice, in comparison, there is not a great amount of difference. When mass producing a bunch of mortices the chain mortiser wins out. But I would rather clean up bored round holes than the scrap left after a chain mortiser. I have done both, I find cleaning up round bored holes with the triangle sections( what is the name of those pieces anyway?) easier because I get to find which way the grain is running, I can't quite put my fingers on it, something about it is just easier.

Tim