I'd like to suggest to provide this pop-up notification only for "long-running installs". I.e. only if the time it takes from the click on the 'Install' button until the installation is complete exceeds a certain threshold (e.g. 10 seconds, maybe even user-configurable) the pop-up appears.
Plus (I almost forgot), whilst I like the fact that the (external) flwget windows are gone, I wonder if it would be possible to include a download progress bar into appbrowser (at a later point in time).
[EDIT: added the last paragraph]