I don't see why it would not fit other than not being able to run the box tune. If you did the TIY kit with flash pro and a tuner you should have no issues. I'm 99% certain that is their issue. The kit, blower, piping, injectors, etc....and engines are the same. They just haven't test fit the system on a 2012+ Civic. Most likely I would bet on that being the case since flash pro was not available until recently.
Also, the 2012 with the AT should work, the 2013+ with the CVT probably will not be able to handle this kit. Size wise I also have no idea how much more space the CVT takes than the AT. I know the new WRX has a CVT option and is making a lot more power than this car and SC kit would but, the CVT is pretty new and people really have not tested the limits of it yet. I would hate for someone to blow up a very expensive CVT without the means to replace it after. Warranty will definitely not cover anything you do to your car once you install the Jackson SC.
One thing to consider depending on your transmission:
The AT unit is much larger than the manual version of this car. The intercooler piping with the kit has not been designed to clear the AT. If you have an auto you will not be able to run the intercooler/race kit setup. That limits how much power you can make. The manual trans guys have a lot more space in the area where the intercooler inlet/outlet piping goes.
I am unsure if the fitment is due to the ATF warmer, which can be bypassed and removed altogether.
Also, I've been on the fence about this upgrade for a while. If one of you guys wants to pull the trigger on this kit and it doesn't work, I would be willing to take it off your hands for probably near full price. Other than the FP you would have to buy, I would be willing to help out with anyone who wants to try and be the guinea pig and runs into a worst case scenario.
EDIT: Plus
@Jake LXer and
@Twitch , you guys are both from NY. I'm from upstate so worst case I drive up and meet you guys somewhere, do the parts swap, and then head back to Syracuse for install.