You have to look at it the way ZEX does... They wrote this manual with one thing in mind... reliability. They do not want your motor to blow with their product installed on your car. Thus, they inform you of all saftey precautions and general do's and dont's. The majority of their testing was done on stock motors with this kit. So, naturally they are going to advise against it. I dont see in the manual anything specific about the Apexi NEO or any Fuel Controllers. I would do some more research and find out if anyone is having problems running nitrous with your setup.
Probably the most important part to remember:
Start with the lowest power level nitrous jet and corresponding fuel metering jet. Make a full throttle pass and read the plugs. Not enough nitrous/too much fuel results in a sooty, black plug coloration. This coloration means that the fuel mixture is too rich. Too much nitrous will exhibit high heat in the form of a bluish or rainbow-like coloring on the plug's metal surfaces. This means you're engine is about to, or is, detonating. Check all plugs! not just one or two!