You just named the main difference! lol
Agnus is the gal responsible here and coupled with a motherboard jumper, determines which mode isto be native.
When I had a PAL A1200, I liked that it booted straight into PAL. Most of the games and such floating around the internet seem to be in that format. But technically, you can switch any later model A2000 between PAL and NTSC rather easily. With a program such as Degrader or Early Startup if you're running Kickstart 3.x.
Just be sure you have a PAL capable monitor if you want to switch to the 50hz standard. Most of the 1084's (any flavour) do a nice job. 1080's distort the picture some.