Air in brake lines and scoring on pistons at annual

[Loman]

We are doing the second annual on our RV-7 and have noticed air in the brake lines and scoring on all four master cylinder pushrod/pistons. We have bled the system but every time the brakes are cycled they appear to be sucking air into the supply side. There is about 6 inches of air there. Because it is the supply side, the brakes still feel fine. The set-up is standard Vans.

Has anybody come across this before and are the air and the scoring related?

These Matco master cylinders appear to be designed to be used the opposite way up. There is no dust shield around the pistons.

[N427EF]

Seeing air in the supply brake line seems to be fairly common.
I am surprised no one else had a comment yet.
I had the same in my RV-8 where air pockets were visible in the translucent nylon lines. This did not affect the brakes as long as there was enough oil in the reservoir to keep the air from getting sucked into the brake cylinder.
I now have steel braided lines and don't know if there is any air inside of the supply hose.
As for your scratches on the pushrod/pistons, don't know anything about that.
My guess is, if the brakes work fine and you don't have any leaks you have nothing to worry about.