I figured out why I was getting blobs at layer change regardless of retraction.
The M700 command which sets filament diameter for velocity extrusion appeared at the beginning of every layer/area. It was not set to be 'synchronized' by default. The trajectory planner can only handle 'synchronized' commands.
That means every M700 command would break path blending, causing a pause to occur while the trajectory planner started path blending from that point on over from scratch.
It also appears way more than needed, essentially setting the filament diameter the same, over and over.
I will need to fix this in the custom branch of Slic3r to do it right. In the mean time I've just set all M700 commands to run synchronized. There are probably scenarios where this wouldn't work right.
Spun two of the liners while polishing/reaming them out in the new print head, so it leaks. Fix is another new hot-end. This weekend probably.
Edit: Turns out I was wrong and the real reason I was getting the blobs was related to my code, not the stuff in Slic3r. Same underlying cause, with the trajectory planner having to recycle, but it was because I was using a letter reserved for other purposes when I defined my M163 gcode handler. Oops.