Some further notes:
I also noticed that I didn't have a Hypothes.is svg icon for syndicating there. So I swiped the habr icon from the plugin's svg folder and copied it as a new file with the name hypothesis and changed the title attribute from within the file. I then added a hypothesis line to includes/simple-icons.php and the appropriate line (as above) in includes/class-syn-link-domain-icon-map.php. This seems to work a charm, though I may go back and use Chris' alternate example so I don't need to rec0de for every plugin update.

These should work temporarily until I can get the appropriate .svg files and create a PR for the plugin directly.