What is TApplication.Handle?
The reason for the application window has a bit of a sordid history. When developing Delphi 1, we knew we wanted to use "SDI" (windows scattered all over the desktop) ui model for the IDE. We also knew that Windows sucked (and still does) at that model. However we also noticed that Visual Basic at that time employed that model and it seemed to work well. Upon further examination, we found that VB used a special "hidden" parking window which was used as the "owner" (Windows blurs the notion of parent and owner at times, but the distinction is similar to VCL) for all the other visible windows.
This is how we solved the "problem" where the windows containing the main menu was rarely ever focused so processing Alt-F for the File menu simply wouldn't work. By using this central parking window as an intermediary, we could more easily keep track of and route messages to the appropriate windows.
This arrangement also solved another issue where normally multiple top level windows were entirely independent. By making the application handle the "owner" of all these windows, they would all behave in concert. For instance, you may have noticed that when you select any of the application windows, all the application windows move to the front and retain their z-order relative to each other. This would also make the application minimize and restore as a functional grouping.
That is a consequence of using this model. We could have manually done all this work to keep things straight, but the design philosophy was to not re-invent Windows, but to leverage it where we could. That is also why a TButton or a TEdit is really a Windows "User" BUTTON and EDIT window class and style, respectively.
As Windows evolved, that "SDI" model began to fall out of favor. In fact Windows itself began to become "hostile" to that style of application. Starting with Windows Vista and continuing to 7, the user shell doesn't seem to work well with an application using a parking window. So, we set out to shuffle things around in VCL to eliminate the parking window and move its function into the main form. This presented several "chicken and egg" problems whereby we need to have the parking window available early enough in the application initialization so that other windows can "attach" to it, but the main form itself may not be constructed soon enough. TApplication has to jump through a few hoops to get this to work, and there have been a few subtle edge cases that have caused issue, but most of the problems have been worked out. However, for any application you move forward, it will remain using the older parking window model.