Hi Sander,
I don't see why the PC needs to pop up every time if the user doesn't want it.
It doesn't. From the main menu: Edit > Global Preferences > Miscellaneous Process Settings > Console window delay. Enter the elapsed time in milliseconds before the console is shown automatically when a process is launched. The default value is 750 ms, and the maximum 60000 ms. For example, if you enter 5000 (five seconds), the console will only appear during quite long processes, provided your machine is reasonably powerful. My intention has been to provide good control over the automatic behavior of the console.
PixInsight includes three different user interfaces integrated into a single environment: a graphical interface, a command-line interface, and a scripting interface. As far as I know, no other imaging application has been structured like that. The console shows the heart of PixInsight because it demonstrates the versatility and modularity of the platform: a GUI and a CLI seamlessly integrated, coexisting and working cooperatively (or that's the intent, at least).
My decision about a minimum console window size was because I don't like to see a 16x16 px console window (for example) appearing on a tutorial. That doesn't make any sense, and demonstrates lack of understanding of PI. Of course, I'd have nothing to argue about a tutorial where the console never appears because the author has selected a long delay time —although I prefer the default behavior.