You are spot on about the S, not sure why I made such a bad error. Looks like I essentially joined two sentences together. But yes the reference area applies for the wing, and rest of the sentence is fine.
Trust me you don't use cross sectional area for a wing for reference! Typically you can use planform area, as I suggest in my post (use wing span and wing chord) or if you can be bothered use a wetted area. It is essential you keep reference lengths the same though for all the calculations, or you need to non-dimensionalise all your values when transferring between calculations.
And no, we have not quoted the equation, for the very reasons mentioned above. For a non-lifting body such as a fuselage, or a car body, people typically use frontal cross-section. Thus if you look for empirical cl/cd's, as I assume was done in this case, you need to keep reference the same hence by point. However a lifting surface you always tend to look at planform or wetted area, thus empirical data will also be based on this, thus you need to use the standard lift equation I stated above.
As for ISA, there is a reason in aerodynamics we use it. There is no such thing as standard! Simply assuming ISA at sea level makes life infinitely easier. ISA was set based on North American and European averages so it's as good as it gets for an average day. Hence everyone else uses it, and if you pull from dimensionalised empirical data you can almost be assured for race-car that ISA was set at sea level, thus non-dimensionalise, transfer to the rc car and then dimensionalise again but with the new values.
As for CFD being complicated, it really depends on methods. Sure you can run an Euler, Reynolds-Averages Navier-Stokes..... and they take hours or days even on the big cluster machines at work. However the basic methods I stated don't require griding or computation, just plug in some numbers and get a result. It won't be totally accurate, but it's not as if an aircraft is being certified. Being in the ball-park I imagine would be fine.
As for wings being used in RC, I have never seen a proper wing being used in RC so your argument about NACA sections falls over there anyway. If it was me, I wouldn't even use an aerofoil and just do flat plate theory, much easier. Typically you get spoilers on RC cars, so if this guy is trying to work out aerodynamics of a spoiler he is wasting his time using the lift equation. However judging by the fact he has gone to some effort, and done quite well minus a few mistakes, I assume he would be using a custom/special wing of some kind.