Exactly this. When they put this LFF (Looking for flashpoint) system in my only hope is that it stays far far away from cross-server. Now about the teleportation part. Flashpoints in SWTOR are located at the Empirial Fleet (donno what the name of the Republic counter part is). They are all tugged into one area. As far as I know there isn't an instance in the world like in wow where it's located. So when you want to do a flaspoint come launch you simply go to that area and find a grp. This is why, imo, it really doesn't matter if you get teleported.
Their warzones (bg's) are already like this. Que up anywhere and get teleported when the que pops.