I don't currently use the Modulus, but I do use another companies jig and I drill my pin and safety holes partially before I start milling the pocket out, I go about a third of the way into the receiver, then I use them basically as a depth gauge as I am milling, has worked out for quite well, just finished number three and getting ready to start number 4 doing it that way.

Also, I start out with the 3/8 end mill and when I start getting far enough down I change to a 1/4 end mill to be a little more precise on the corners and edges, my 1/4 cleans the pocket up real nice.

It doesn't square them out, but it does give you a bit cleaner cut with a smaller radius, nice and clean, I started doing it because the 1/4 is cleaner in its cuts than the 3/8, I am picky on how clean my cuts look and I seem to be able to manage the small bit better.  Just something I do, and others may hate it.  Still leaves enough radius with cleaner walls is all.