When I open a popup with a dock present, it overlays the dock. How do I keep that from happening? Shouldn’t the popup respect the dock just like a normal view does?
No. Popups are not "View-aware". Any Popup positioning is done with respect to the Page.
There is no way to keep this from happening 100% of the time but you could, in theory, place a property within the Docked View (or session) which tracks whether the Docked View in question is open, and then use this property to determine where the Popup should be opened.
I would like to add a feature request to make popups (optionally) dock aware.