Hi @MatthewDunn,
I guess a couple things here...
First just in case you're not aware, the community is mostly a user-to-user space. While there are some Instructure employees who monitor and occasionally post here, it's not a common practice so I don't know that you'll get a direct answer from an employee here.
Second in regards to your questions about display, I don't think you're ever going to see an exact replication of the view in Speedgrader/DocViewer as a download. Those views are interactive HTML, where things can scroll, move around, etc as needed. A PDF is meant to be a rather static format. The PDF download, as far as I cna tell, is trying to maintain the original document formatting, size, etc. In order to make comments display exactly as they do in Speedgrader, the document would have to be shrunken down, which some people may not like. Long comments also scroll in Speedgrader, and you can't realistically have something that scrolls in a print format since you can't scroll on paper. That's why the PDF just works differently. Now with that being said, when viewing in Adobe (not the printed version), the annotations do look more similar to speedgrader with the full comments on the side:

This is why I think part of the issue may be in certain viewers. Because this is really taking PDFs to the next level, I don't think there's a standard way the comments.annotations are displayed. Some PDF viewers may handle it better.different than others.
I'm not a PDF expert at all, but I have a feeling that "not printable" flag your viewer is showing is more about preserving the document formatting and just the way PDFs work with comments more than anything Instructure is deliberately doing to reduce functionality. I think it's up to each PDF viewer program to decide how they'd print comments, and I did show the example of how Adobe does it. It's clearly not the same exact view as shown in Canvas, but everything is there.
Maybe someone else with more expertise in PDFs can chime in here, I'm just trying to help out as much as I can.
-Chris