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Yes, such an output setting can be made with the config tool.
I don't know how to configure the MK3 but your calculation doesn't quite match reality. Pal is more like 288 lines and every game possibly can have the full resolution/overscan or something like a 200/256 line window within these 288 lines. And the position is not the same on every game, which makes integer scaling with a perfectly centered picture and the least amount of wasted space a bit more complicated.
with 1080 visible lines, you can of course go up to 270 source-lines and no black borders added by the flicker fixer (at least not top&bottom). We've had a similar discussion about possible 50Hz modes in another thread, where a 540p output mode was suggested to keep the monitor from scaling and keep memory bandwidth low at the same time. If you can live with black borders left and right on a wide screen TV or monitor, then a 1080-lines panel is almost perfect.
I don't know how to configure the MK3 but your calculation doesn't quite match reality. Pal is more like 288 lines and every game possibly can have the full resolution/overscan or something like a 200/256 line window within these 288 lines. And the position is not the same on every game, which makes integer scaling with a perfectly centered picture and the least amount of wasted space a bit more complicated.
Mine was an example, but you are right, 288p with integer scaling will only fit x3 inside a 1080p frame. It will leave quite a large border. Unless it is possible to display the image at x4 anyway and crop out a few lines?
Unless it is possible to display the image at x4 anyway and crop out a few lines?
Yes, that's also possible - both with and without the config tool. The live configuration allows you to move and scale the picture while the game/demo is running. This is a major improvement over previous models of this flicker fixer, where you had to guess what a good setting would be, store it in flash and hope that your guess was good when loading the game.
Live configuration is indeed very cool and solves quite some problems.
I was the one brining up the 540 line resolutions (exactly half of 1080p). So that's twice the regular PAL interlace vertical resolution of 512 lines plus a total border area (overscan) of 28 lines. Of course if you don't use interlace it's 256 x 4 plus some extra lines.
In general, this works very well as games mostly stay close to the normal 256 lines. Back in the day, most people set up their CRT monitors to use only modest amounts of overscan, especially in PAL mode. (Overscan is the extra image area around the regular image size that extends below the edges of the screen. The Amiga lets you use the some of the area normally used for overscan to make the useful image area larger.)
288 or 576 lines doesn't make much sense, as this shows much more image area than any regular CRT monitor would display. These numbers are just the maximum that can be encoded by digital video. Unless I'm mistaken, the Amiga's limit is also a few lines less than this.
NTSC is a bit more difficult. One resolution that works reasonably well is 1440x900 / 2 or 4, so 400 + 50 lines for interlace or 200 + 25 without interlace. This is not pixel perfect but I find that my displays do a good job of artifact-free non-integer scaling.
However, 1440x900 is a 16:10 resolution, so the pixels won't be square. Still, on the Amiga NTSC pixels are supposed to be 44:52, so if you display 1440x900 as 4:3 you get pretty close to the intended pixel aspect ratio. But I believe most games ignore all of this anyway, and it's not too important in practice. On an analog CRT the aspect ratio would have been off by a bit anyway.
I've also been thinking of NTSC 216 x 5 = 1080p. This should be 1920 / 5 = 384 pixels horizontally (with square pixels) which might just about fill the screen without any black bars on the sides. But I haven't tried this yet.
While the info about pixel aspect ratio comes from a very credible source - the Commodore Developer material - I am pretty sure that it was hardly ever used in practise. My version of the 1084 monitor had the X-Size and X-shift controls on the front side, so I just fiddled with it until it looked good - I remember shifting left/right on a regular basis, depending on which game I was playing. This was the one observation in my memory that brought me to adding the live config feature into Indivision AGA MK3 - if it was necessary back then, it's likely to be necessary today.
It was surely nothing like the MACs that came with pre-calibrated monitors that would even report their size to the main machine, so WYSIWYG would really be the same size as the printed paper. Or I never heard about it - the only word processor I ever used was Word Perfect, and that didn't have WYSIWYG-view.
So the "roughly 20% difference" in aspect ratio will most likely result in a different perception of the fixed-size fonts: USA-based users will have a different memory of the appearance of the Topaz-8 font than European users. The good part is that - knowing that most monitors had the X-size control easily accessible - we only need to resemble the aspect ratio - there is no need to be on the spot. Further, you can achieve this two ways: You either deviate on the X- or the Y-axis, and for both, you have choice of using the Indivision's scaler or the monitor's scaler, depending on what produces the better result. Four permutations to try 
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