I realize now, I just did not go far enough down that page when I was looking at it yesterday.
This morning, I tried installing from the source the new release of this, and seemed to get a good install. When I went to go to the Moodle main page, I got nothing but a bunch of debug info.
I then substituted the files from your site, and now have it working. With debug on, I still get a bunch of debug info, but nothing fatal. I will look some more later, but have to go somewhere right now.
I took a quick look at moving the the left margin over like you illustrated in the picture. Using Bonfire, I can do it but have not been able to find WHERE to make the changes in the actual files. I did find that it will probably be in yourmoodle/blocks/marginalia/annotation-styles.php and I think it might be line77. However, I can't see any differences when I change that line, even after purging cache files and using theme developer mode. Maybe it interacts with other parts, I just don't know right now.
I will play with it some more when I have the chance.
Thanks again for the working version,