The water pump in MY personal ST1300 (07) was pressed in (by me) with the 24 mm depth and has been working fine for over 100,000 miles so far, and has no scrape marks on the inside cover, or strange noises.
I'm thinking that the way they pressed it in, has more to do with the damage done, than the depth that they pressed it in to.
Perhaps they didn't SUPPORT the bearing when they were pressing it in, and that is why they pressed the bearing out (which changed the depth) and why it struck the inside cover.
I still say they may have damaged the bearing/impeller shaft, and those parts should be replaced as well.