Dan, I'm also a civil engineer & will reiterate what some others have said. Any project that requires DOT permitting should get them involved early on and have a level of coordination to get their immediate feedback on the site plan. When we do this, we also include the developer in our meeting so they can hear the DOT's concerns/comments firsthand. This predevelopment meeting is done before design because they can be so impactful. For example, even if you are complying with their criteria, what if they have a road/ROW widening planned in 2 years that nobody knows about that eats up 30' into your property.
If you are going 'by the books', the Civil could have dropped the ball on this. If they are rejecting your permit because of the sight distance, it is worth understanding their experience with this DOT and how lenient they are on design exceptions. Some design criteria can be really tough on a developer, and I have had many instances where DOT will allow us to do things that are not exactly meeting their code. And if your sight distance is only short by 15%(?) of the requirement, that could be a reasonable variance with some DOTs.
Sorry that may not really help out your situation, but just thoughts from another engineer.