Mr.B (and everyone else who is trying to follow) - let me give one simple example:
The Amiga with it's "Hires interlace plus a little overscan" screenmode comes closest to 800x600. Indivision will take the maximum overscan area of 768 Amiga- pixels and write it into an 800x600 pixel framebuffer.
This framebuffer has two ports: One write-port (for the Amiga-side) and one read-port for the monitor output.
The monitor output is now reading the 768 pixels width, but pads a few black pixels to the left and to the right in order to reach full 800 pixels. This will bring the output to a standard resolution. The same happens to the number of lines - the output "processor" will choose whatever PC screenmode fits the Amiga screenmode best. In addition to that, you have control through the conifig tool: If you want to change the number of padding-pixels, you're free to do so. For example: Your screen seems to have a native resolution of 1920x1080 pixels. This is more than the Amiga can display. However, you want the screen to not scale at all, so you give it a non-standard screenmode of - say - 960x540 pixels. If your monitor isn't too stupid, it will display pixels with exactly 2x2 native pixels.
I can freely program output modes. Indivision AGA MK2 is based on an FPGA, which is launched from flash. This means that whenever I add a new screenmode, I can distribute a new flash image through my website. After you've updated your flash, the new screenmode is available to you. If at some point a new type of flat panel becomes available that has "the" killer resolution that everybody wants, I can support that in Indivision AGA MK2.
Got to go to bed now. Tomorrow is pre-screening day (EMI test - yay..).