There have been a number of requests for pen support / markup support in Logos that would allow the user to mark up a text in a more natural manner.
Adding pen support would require a lot of planning and programming, I assume. However, there may be a simple(er) solution that would appease some of the pen-advocates.
Add the ability to visually connect highlights, like so:

Might want to reduce opacity of the connecting line to something like 30% (as pictured here):

As for how this would be handled in the notes: either (a) this will be a unique linking-style highlight or (b) it would be an independent feature which could be added to any note (highlight). What I have in mind for (b) is a third option alongside these two:

With (b) any two highlights could be linked and maybe linking would combine what would otherwise be two files into a single file with two anchors?