PY:
Advanced classes cost money for supplies & teachers. The schools have made the decision not to pay for these, and therefore have lower tuition.
I also think that the boys schools in the five towns (specificly DRS of which I know a little about, but others to a lesser extent), as well as a number of the girls schools there, do allow a child to prepare themselves for excellence in both/either Kodesh or Chol (to use your terms). The costs are also more than triple what has been posted for an average brooklyn school (for DRS).
Where I am, the boys yeshiva HS do not have “Chol” up to the level that I would like, but at least the schools do take it seriously enough that a graduate has the ability (if they apply themselves in HS) to go to a normal college if they so desire.