The transformer won't know PAL from NTSC, just AC voltages in, and AC voltages out.
Yeah the A1000 will still be NTSC, which is annoying as it can't be switched to 50hz. I don't know if replacing the Agnus with a PAL thin agnus will allow you to run PAL software, there was a board that allowed you to run a fat agnus in the A1000 too.
I'd probably sell the NTSC A1000 and look around for a PAL A1000, if I were to keep the NTSC A1000 then I'd prefer the power supply to be standard 110v and use the step down transformer (just for authenticity).
