How did you find out about your scarring, was it a civilian or military eye doctor?
I went through both MEPS and three full flight physicals in Corpus over the course of a few years when I was applying for OCS back in 2004-8, neither place ever found any issues with my eyes. I was selected for pilot and when you first reported to OCS they sent all of us Pilot/NFO types to medical for a more "thorough" screening. They did a dilated eye check there and told me they found a small hole (scarring) on my retina, and that it could possibly disqualify me for pilot. I was told the same thing; that I probably got it from some form of head trauma from sports or getting into scraps as a kid. I continued through OCS for the next 8-9 weeks or so while my package was reviewed by NAMI (honestly that was more stressful than the DI's), and they came back with a waiver for me shortly before graduation.
The conditions of the waiver were that I had to have a thoroughly documented fully dilated eye exam every year during my flight physical to ensure the condition didn't begin to degenerate. Their concern (I was told) is if the condition worsened to a point, certain stresses such as pulling G's could cause a weakened retina to detach (which might make it a little tough to land a jet in blinding pain with no depth perception). When I got down to Pcola I was examined again at NAMI and the eye doc told me I could have laser eye surgery to fix it, but as long as it didn't get worse or bother me it wasn't completely necessary. The only time I ever noticed anything would be occasionally during BFM, with certain sun angles if I was straining to look behind me I might see a small black "floater" similar to what you see during the eye exam when they shine the bright light into your dilated eye. Other than that I never had any issues and it hasn't gotten worse on any subsequent exams.
Bottom line, the condition is waiverable (or at least was recently) but it's not black and white. Several factors could play in such as the severity of your current condition, the subjectivity of the flight docs examining you, whether the approving authority got surprised with a quickie on their way out the door that morning and they're in a particularly good mood, etc. There's also the fact waivers generally tend to get more easily approved the further along you are in the journey or the more money Big Navy has sunk into you. Being only an applicant it'll be tougher than if you were diagnosed in the fleet later on, but keep in mind I got my waiver approved while I was at OCS and wasn't even commissioned yet, so I was only one step ahead of where you are now and the only money they had invested in me was for a 'war spoon' and a shit ton of blue powerade.
Trust me, the Navy wastes plenty of time/money on other things to worry about you costing them a few shekels for a flight physical. Go apply, get the physical and see what a Navy flight doc has to say about it, then go from there. Good luck to you