I'm not surprised. And how stupid is that? This is a fairly common theme in other areas I work in. Local building departments seem to expend most of their energy on commercial concerns and new construction. Trying to tie them down to make a statement that can benefit their local homeowners is near impossible. However, there is a flip side. Imagine the guy who is replacing his roof out of pocket, no insurance. If the City enforces that code, they are forcing that guy to spend another $100 plus per square because he has to replace all his decking. I think that is the reason they don't enforce it.
One thing you can try is to demand that local official to give you a written waiver stating what he told you. I'd tell him even though you're essentially getting screwed by their ruling, you're okay with it. However, you need to have something in writing so there is no chance it can come back and bite you in the future. I've had this conversation with these guys before. "Mr. Building Inspector, if you are saying you aren't going to put something in writing so I can get my insurance company to pay for it, then I need you to put that in writing so you can't come back on me during or after the work is done." "You can't have it both ways pal, either you're for it or against it, but when your written statement requires it, I need a written statement that you're not going to require it for me." See what he says then. If he won't do it, talk to his boss. Take it to the Mayor if you need to. These spineless, lazy bureaucrats need to be painted into a corner sometimes before they'll do their jobs.