Well, for obvious reasons: when n is odd, and the row R is even (specifically, 2 mod 4, i.e. of the form 4k+2 for some k) and the column C is odd, then even if gcd(R, C) = 1, the set being considered contains only even numbers — note that it starts with R(R-1)N/2+C which will be even as R(R-1)/2 is odd and so is C - so you won't have any primes in it. (That is, you'll have a red cell, even where the gcd pattern has a black one.)

And when n is even, there's also a heuristic argument that there are only finitely many counterexamples; i.e. you should expect to find the pattern from your process exactly match that from just the gcd, beyond a few counterexamples: https://news.ycombinator.com/item?id=17106648