Geoff - Yes, there is a bit of width variance I unintentionally introduced when sizing the muntins. They were ripped instead of planed to their final width. This sets up for variability in the ripping off the waste, and whether the saw cut is flush to the more accurate shaper cut. I clean this up with a lick or two of a handplane, but is something I prefer to avoid, but I don't like to over cut either. It is all about where you choose to reference from, and the accuracy used to get to that point.
This is an ever-evolving sequence, and it has changed a lot over the years, but still has a few rough spots. I enjoy using the plane, so I'm pretty happy with the method as described, but a fence on the saw (or shaper?) that allowed the muntins to ride on the bottom of those plows/rebates would be a fine next step. Then I'd have to come up with another place to use the handplanes...
The glass rabbets on the stiles are done on the shaper. In the cutter set (brazed, custom made by C G G Schmidt) I designed, I also had bearings made so all this cope and stick can be done on curves, or mated with any cutter for subsequent cuts. I set up a tension fence to hold the stock down on the table and pivot the front of the stile into the cutter with a bearing to make a flush cut. Push until I hit my mark and stop and withdraw. For short parts, like the transom stiles, I set a tail block on the shaper to start my cut and the push to the mark, back up a bit and withdraw. This keeps the smaller parts from sudden over feeds and kicks. A router can be used, but is slow and noisy and dusty. A moments inattention, and you can ruin a part. The shaper prevents an overcut, for the most part. Once the sash is assembled, the corners are squared up with a chisel, though my co-worker likes to use a bearing over a flush bit in a router for all but the last 15% of the cut. I think it better to have one method for that operation instead of going over everything twice, but then, I'm also picking up the handplane elsewhere. Different strokes.
While we have to be slaves to the dimensions, the safety, the accuracy, the budget, the tools and machines at hand, we can find little areas to strike out into and enjoy a bit of creativity, or just do some pleasurable handwork.
If the sash is all glass work, it is possible to set up with sticking on only one side/face of the sash, and then run all the parts with single copes and single stick. But the double cope does add glue surface, and makes the joint fit up so much nicer, that we almost always do the double copes/sticks and then rabbet.
If you ever want to sell your work, make up a cope and stick, mortise and tenon joint and cut the two parts to about 4-6" long and hand it to your prospective customer and let them fit it together and pull it apart. If that doesn't sell them, then nothing will.