Point is also that the particular screen I use for that setup will not work with Vsync from my ECS V3s or VIC II sync from my Turbo Chameleon 64 V2s so I highly doubt it would work with AGA MK3s Vsync.
Same message for you: Use AutoResolution, it will have the same number of lines every frame, just like you've programmed for your MK2 unit. No guesswork - if the monitor supports 50Hz, then AutoResolution is *very* likely to work, and it's perfectly V-Synced.