I've been spending waaay too much time on this D2005 VCL change. The intent of adding this property was certainly a noble one. You can read more about the reasons why this property was added in
Allen Bauer's blog.
In practice, however, this change has caused me much grief. For example, I have some components that override the original WndProc to do some custom drawing. Since the PopupMode property now can cause forms to be recreated, that means that all the controls on the form will be recreated. I'll now need to trap recreate events on the component's form and figure out a way to remove and re-add all of the custom WndProcs to the current list of components that have their WndProcs overridden. It also caused some problems by causing a WinRunner form to briefly display before our splash screen. Setting the PopupMode to pmAuto solves a lot of the problems, but by then, I grew to loathe this new property.
I'm all for progress, but I would have preferred that any VCL changes made that cause forms to be recreate would preserve the legacy behavior as the default value for this property (at the very least).