Plenty of elements of the yeshiva world have constituency who wear other dark colors besides dark navy/black. If someone goes to a yeshiva which a segment of the bochurim wear blue, gray, or other colors….that was never the issue under discussion here. I also don’t think you would want your sons to dress differently than everyone else; you’d probably suggest changing yeshivos to find a place where they fit in rather than be contrary to what the entire Yeshiva is doing.
I take issue with the insinuation that the reason why a rosh yeshiva did not reprimand you or your boys was because you were paying tuition. If you respect this rosh yeshiva as an authentic daas torah to the point where you entrust your boys to him to guide them and teach them Torah, then you should not think of him as anything less than what the Torah demands of chachamim – sonei batzah, etc…people who are unbiased and not motivated by money.
If you think that all the rosh yeshivos are impacted by money and that money will make you invulnerable… it’s sad that there are rosh yeshivos who are like that, but it is an affront to Torah to say that most or chas veshalom all are such.