Yeah, there's the two separate issues going on. As long as the difference in color is not somehow confusing, I think you let them play. I have had one game where the JV and soph. jerseys were completely different colors (one red, one silver) from each other, but both sufficiently different from white that it did not cause the players any grief. Just me. I called a foul on a rebound where a kid in red went "over the back" of a kid in silver. I felt silly.
OTOH, the difference 3-4 v. 3-5 is significant. Uniform and apparel are distinct and specific categories. 3-4 regulates the uniform. If the uniform is illegal because it does not conform to 3-4, then 10-5-4 comes into play. 3-5 regulates other stuff, including some stuff normally considered to be articles of clothing, that isn't the uniform. If some piece of gear or apparel does not conform to 3-5, the player simply may not play while wearing it.
It may seem arbitrary, but I think the reason for the different administration is two-fold: First, the school provides the uniform, and so the school's representative (the coach) bears the cost of violation. Gear and apparel is generally provided by the player, and the rules put the responsibility for this on the player. Second, dealing with an illegal uniform is difficult and often time consuming, as you found out. Gear and apparel can normally just be removed right then and there.