There are 2 phases to plumbing, the stubouts and the actual plumbing. The stubouts are done (usually) before the rebar and it is just the plumbing parts that will stick through the gunite. The 2nd is the actual plumbing done by the plumber.
I think it was 6" from top of the bond beam. The waterline is at the 3" mark.How far down from the top of the gunite do the tiles usually go?
I did check with my cousin because I'm always comfortable in his pool - his are 9" and he said he has one spot that is 11" and people always complain about itI obsessively researched pools for my project and your concern is a fairly common complaint. Many people are uncomfortable with 12" step height when the pool is empty because 7" to 8" is standard outside a pool (like indoor stairs or patio) and they have to work much harder than normal.
However, you have to remember that when the pool is full of water you weigh less. Walking in the empty pool doesn't give you the proper comparison.
If you have any friends with a pool or access to a community pool you should go visit and do your stair tests with water. It may help put your mind at ease or confirm you need the re-work done.
12" is within standard from what I have read....but it is your custom pool and you can change as needed. People with bad knees or older in age may prefer an easier step height.
Have you considered hand rail type system as well? We are putting boulders next to our stairs so people can have more stability as they enter/exit