I think those modes can be output over HDMI/DVI too, as both the FPGA Arcade and the Indivision AGA MK2 have DVI output. We should ask people who have both the Minimig/MiST and the FPGA Arcade Replay, like Laurent from Amedia. I think they give similar results. Compatibility may differ, however.
One important difference is that you only have SCART output with a Minimig/MiST though, not with an FPGA Arcade.
There are pros and cons in both cases !
But I would like to emphasize, again, the fact the screen plays a big role. I remember using my A1200 in SCART mode on a decent LCD TV : the result was HORRIBLE. Similarly, before using my current Iiyama LCD, I had horrible results with a Minimig and an LG LCD monitor : it did support 50 Hz but didn't have the right pixel clone and scrollings were not smooth at all. I guess TVs generally support more modes.
ANYWAY... If you find a proper screen, IMHO, the result is awesome. A great balance between pixellisation and bluriness that is even difficult to achieve with a real Amiga and an emulator (on a LCD I mean... an Amiga looks great on CRTs of course). Probably due to the fact it outputs at 720x576 while also enabling the use of scanlines & filters.
