It starts in a borderless window for a few reasons. When using “native fullscreen” and using Alt+Tab on Vista-7-8-10 - the game will eventually freeze forcing you to reboot your PC because accessing Task Manager will be impossible.
Likewise another issue is that when switching fullscreen resolutions (between 2D and 3D world) the game will often crash before making an autosave after a completed mission and/or adding nothing to your logbook.
It was incredibly annoying losing all progress after an extremely successful 1 hour long mission due to a crash (because you simply can’t have the same experience again and all will happen differently). And the workaround is switching to a borderless window. So my take is that in 4.34 and up borderless window is a default option just for exactly this very reason.
From what I gather while BMS team moved 3D renderer to DirectX11 - the 2D one is still that ancient GDI-based 1998 tech.