Hi Brett,
The edit-while-zooming issue isn't a deal breaker; I'm sure that there are higher priorities than addressing this little issue, especially if its a PITA to do so...
One other (minor) observation regarding zooming: It seems the GUI responds differently in 3.9 vs. 3.8 to Shift+Mouse_Wheel. In 3.8, Shift+Wheel lets you scroll side to side, while Ctrl+Wheel zooms in and out. Used together, they can be a great way to navigate around a project. In 3.9, Shift+Wheel and Ctrl+Wheel both zoom, and unlike 3.8, they zoom in and out of the upper left corner of the project rather than the mouse point. Perhaps others will disagree, but this less useful to me.
The hierarchy board feature is very nice. I'm using a dozen or more already. I'm sure I'll get into aliases soon as well.
Cheers,
Peter