Shouldn't have damaged the seal which is internal to the master cylinder but will destroy the dust cover.
Beta rear brakes are always a pain to bleed. I find it necessary to crack the banjo bolt at the top of the master cylinder as that's where the bubbles settle being the high point of the system. Also, given the flexibility of the disk, you may have to put pressure on the disk to get the pistons on both sides to be equal. What happens is one piston can be out a little more than the other and instead of self centering like they would in a car with a big thick disk the further out piston will push the disk over to the other piston. This makes the brakes soft. The way to check it is to actuate the brake with a finger on the edge of the disk near the caliper. If you feel the disk move the pads are not properly centered. If it does apply the brake and gently apply pressure opposite to the movement of the disk. Remember you're just pushing the disk back to center. Don't use any kind of tool as you don't want to bend the disk. It might take a few times. The end goal is to be able to apply the brake and not feel the disk deflect but stay centered between the pads.