I'm having trouble envisioning what you're describing. The property inspector can be closed using the following command.
inspect -close
To explore what you're descibing, I created a custom UI component using ComponentContainer and made it available in appdesigner using appdesigner.customcomponent.configureMetadata. After dragging the component into the app in Design View, I assigned a ValueChanged callback function to it and placed a break point within that callback function. After running the app, I interacted with the component to trigger the callback and was able to see component property values from within MATLAB desktop.
Update
I figured out what you are seeing. I believe you are accessing the object by double clicking on the object from the Workspace browser. This indeed opens the Property Inspector. Use openvar to open the variable in variable editor. If the object's name is "comp", openvar('comp').
