In this case, it is requiring a larger screen resolution than what you were running with. And the solution is to either increase the screen size, or adjust and save the settings like you mentioned. Most window managers will not let an app display a window that is larger than the screen, so for the less experienced users the solution would be to use a more sophisticated window manager that handles this. Most window managers do, even the smaller ones like Icewm.
I do see a default config file in /apps/gentoo/etc that might allow to set a smaller default window size on app launch. But there are so many other apps and pop up windows that are larger than the screen with the simpler WM's, the "save file as" window in Firefox does this on me with my 800x600 display. So even with setting gentoo to accommodate smaller displays, there is still a host of other windows and apps that would show this behavior. Best solution then is like mentioned above, increase screen display or use a WM that handles the issue.
I didn't pay attention to the generic X icon, and as we concluded earlier that is in the realm of the upstream app maker to deal with or not deal with.