You asked for specific reasons as to WHY docking or collapsing the navigation boxes are important (beyond just enjoying more space).
For me, having the boxes there impedes functionality in two very specific instances:
1. When I am grading, I like to open two windows - the student's activity reports, and the grade book. I could easily check on all assignments and mark them accordingly this way. Now that I am unable to dock/collapse the nav boxes, the two windows no longer fit well in the screen (the two nav boxes in each window take up most of the space). This makes grading more time-consuming and frustrating than it needs to be.
2. I used to make PDFs of my student's grades for reasons such as transfers, for documentation, and so on. I could collapse the boxes and produce a usable document or file. This is no longer possible because the boxes clutter the page with information not appropriate for sharing with outside entities, and it changes the way the grades fit on the page (it no longer looks professional).
It was so disappointing to get an "upgrade" that made using the Moodle less efficient and usable in these important ways.
I would be very happy to be able to dock or collapse the boxes again.