...It's normal for the anodising on the inside of the bearing cup to have some marks on it as that's normally the bearing being squeezed into the cup as it's supposed to be tight.
The bearings in the cups are not tight, they can slide in quite easily by hand, perfect fit. Only way the anodization of the cups would wear off is from repeated movement between the outer race of the bearing and the inside of the cups but under normal circumstances (cups properly aligned with each other) the grease should prevent that.
I'll certainly bow to greater knowledge than me on this as my experience is based on 2009 super record, 2011 record and brand new P2M NG. The cups in the super record and record are different materials and the marks as such on the super record are from getting the cranks in and out. They've never been slide in easy by hand and when trying to remove them they've always had to be wrestled out even when one side has come out so not just down to the hirth joint locked together. I remove them at least annually. The record cups have been far worse and the drive side has marked up quite a lot. Whether this has been caused by me having to wrestle them in and out it's possible. Both are fitted into threaded bbs and both remain incredibly smooth and silent once in. They've got 1000s of miles on them so pretty impressive overall. Historically I've only ever used a thin oil in between the cups and the outer of the bearings so I'm interested to see how the morgan blue works now I've just started using that.