You'll be able to select (in software) either a 50Hz or 60Hz video mode. This is important because 50Hz VGA will not work on most LCD/TFT monitors.
You'll be able to use the WHDload NTSC tooltype to select PAL60 and it should work well.
Some games which use the VBL instead of the CIA timers for music replayers will sound a bit strange ;-)
I am not exactly sure how bit 5 of BEAMCON0 did what it did in the ECS agnus, but after the boards arrive and people start actively working on updates information will flow.