Quite weird request but easily doable because ECS Denise (and AGA) supports configurable genlock color (each color palette entry has genlock transparency bit) and it is already emulated. Simple to make it config file only option.
Not sure what kind of config file entry should be because it should allow more than 1 palette entry index.
But don't expect this to work perfectly, for example scoreboard might use same color palette entry (but different color value) that shouldn't be transparent..
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