Basically either it’s a deal-breaker for them or it isn’t. If they’re willing to consider the “right” candidate who is missing one key attribute, then all you need to do is what you would do anyway…write a well articulated cover letter, customized to the specific needs stated in the ad. If they are not willing to consider you, it doesn’t matter how well you nail the cover letter/resume. And you have no way of knowing that. You do HAVE to apply though if you think you can do the job well…finding a job is a numbers game, and you should apply for anything you think you could do and would enjoy doing.
I can tell you, I’m on the market for about the 8th time in my career and what I know is the opportunity I land is never the one I expect or it’s about the 15th one I thought I had in the bag. You never know what it is that will get you or lose you the job, all you can do is be honest about who you are, what you have to offer, and what you hope to attain in this job search. Now, part of me does say that in this economy (it’s the worst one I’ve ever been unemployed in by far), I’m ending up applying to jobs where I think I’m the perfect candidate because of how uniquely and perfectly I fit their ad, I have a very strong resume and write a very effective cover letter customized to the ad, but yet I still don’t hear back. But then I’ve had in the past gotten a call for something I wasn’t sure about at first, and then bam, a week later I’m working for them. You just never know, but there’s one thing that is 100% for sure…if you don’t apply, you won’t get it, and if you do, you might or might not. Look at it that way and your question answers itself.