I just got a surface pro 6 with pen and I wanted to continue using Paint.NET until I ran into the issue described in this post. I know you said that you has already investigated the issue and hope for a resolution sometime soon but I thought I'd just add my conclusions to my own research. The problem (at least the iteration I am experiencing at 1/27/19) is that windows is applying some sort of "deadzone" when first touching the screen (either with a finger or pen). You can observe this when touching or penning(?) and slowly moving your finger/pen. There is a consistent radius between the first touch (which will ALWAYS register a dot on PDN) and when the software begins to render the line. The radius seems to be the same distance as the short line that first appears once you break that threshold. It appears that the deadzone is supposed to make it easier to access the "right click" menu achieved by holding down on the deadzone area for about a second. This is consistent with the mouse deadzone of 4px that windows uses to protect against accidentally dragging when clicking files. Unfortunately I could not find a registry entry that would allow me to reduce that radius.
The behavior can be observed on any application that is not created with a native ink canvas (hell it even happens on iOS). This is where I think it may be almost trivial for PDN to fix; when I was starting up a project a while ago I originally tried to learn the PDN format to import images directly into my program. That's when I read that all its doing is creating a blank windows canvas in C# and the rest of the inner-workings is completely opaque. I recently read that declaring a canvas as an "ink" canvas would allow the pen/touch/whatever to work correctly and not revert to whatever they would describe as the "legacy" path for touch. Forgive me for the simplistic descriptions as my research was limited to a very high level; even if it were as simple as adding an attribute to the canvas there are almost certainly going to be additional work with supporting brushes, tilt, pressure, and whatever else the native API supports.
Anyway, I'm really looking forward to paint.net having native support for touch. I just purchased the Windows 10 app in hopes that it had native support already but its otherwise great to support a product that I've been using for years since I stopped using Paint Shop Pro 3.0
Thanks, and I can't wait for an update on this!