I doubt they will commit to anything past 1 year of production since no spec or price exists for any more than one model year at a time. If you're asking if you have to apply again or will your application carry over that can only be answered once the application process known. But, don't you think it would be a little unfair to someone who is interested in 2018 to not be able to get a car because they didn't sign up in 2016?
Ford seems to be trying to be pretty savvy about this so maybe they have researched others with similar situations. Here is how the Grand Canyon lottery works: At t0 (the first time you sign up, or after your last "trip", which resets the clock) you start off with 1 point [as would be the case with this application]. If you don't get chosen this year, then next year when you apply you get a point for your last year, building up over time. So in the case of the NFGT, for 2018 cars, having signed up for a 2017 (and not gotten one) might get you extra bonus points as well. We'll see...