Around here we call them "stepped tenons," and you see them on everything from no name basket pipes to higher end English stuff, post 60's GBDs for example. I've never really understood if there was ever a purpose. In 99% of the cases I've seen the mortise was not double drilled to mirror the tenon. Back in the days when filter pipes and contraptions were all the rage, it was very common for the mortise and draft hole to be drilled and a third somewhere in size between the two drilled most of the way into the pipe to accommodate the filter/innertube/stinger. This created a series of three holes drilled from largest to smallest from shank to bowl. Sometimes you'll find a pipe whose step fits inside (never snugly, I might add) that second hole.
I have another theory, but it is only speculation. If you look at premolded stems, even today, that step is cast on many. I think there are several other possible functions for the step: as a size gauge, something to help facilitate the molding process, or for the purposes of lot identification. I'm sure there are those out there that know, but I've never heard a good explanation.
All that said, nothing beats a simple non-stepped tenon.