Slight update. After I got the seam test good, I did a benchy. And there was still some blobs/divots though a lot better. Ticking off Update Machine Definition and Update Firmware Configuration made it more similar to Slic3r's seams benchy. Seems like S3D is doing something my printer doesn't agree with, so now it's running completely off Firmware values. Well, except Retraction settings, you need to Force the slicer to use Firmware retractions, but I don't even know where those settings are in Marlin so I leave that off.
If you want to try that route, you have to be sure your firmware values are correct. Like bed size etc. Or bad things will happen.
I am having the same problem. A line of sharp-edged blobs up the O.D. of a cylinder. The straight cylinder has a thick part at the bottom of 3/8" wall thickness and the O.D. in that portion is OK. But as soon as it transitions to a 1/9" wall thickness, the blobs appear and extend up the 2" height. Actually it places lines of blobs in two places on the O.D.
I tried the same STL file in Cura and it prints with no problems.
I cannot remember that I've upgraded S3D so I don't know where these problems have come from in what was a great product.
I can print a calibration cube generated through S3D and it prints perfectly.
Printer is a Qidi X-one, a very reliable printer.