If you have problems with resource matching try putting 2 Rumors at the Cantina in there. I had built an experimental S&S deck consisting of 2 S$S, 2 Jedi, 2 Rebel Alliance, 2 Rumors at the Cantina and the other 2 neutral objectives.
I never encountered a resource matching problem and the deck played much better than I expected on top of it!
I think that he is referring to the rules and not issues with resource matching.
I agree it feels odd, but you are doing it correctly. That is one part I wish they had done different with the deck building rules. It feels wrong to always run with the affiliation you have the least cards of.