This issue has been bothering me for quite some time.
It seems that while other parts of Moodle are being upgraded and updated, Atto remained with little changes in its core.
On one hand I guess this is probably because there are other more pressing issues as well as "it works, don't touch it" approach. I'm familiar with it myself.
On the other hand, the YUI library, as we all know, is no longer developed and supported.
What worries me the most is the widespread use of execCommand, which have been marked as deprecated for several years now and could very well be obsolete in the near future, who knows.
Maybe it's already in the works, but I couldn't find a discussion here or an issue in the tracker. I'm worried we will be unprepared if any future browser upgrade will "break" the editor.