Teachers should be compensated for their work, considering that most teachers work above and beyond "dismissal time", and often bring work home with them. Charter schools were created to provide alternative educational opportunities, but this doesn't have to mean that teachers in the "regular" school system should not be paid for their time.
The principal and assistant principals of each school organizes the teaching schedule, and the purpose of the union is to protect the teachers from being exploited, although corruption exists within unions as well.
If the principal of each school is responsible for the allotment of the budget, there should be some negotiation with the teachers who are available to teach longer hours, and the union.
As far as charter schools getting more funding for a longer school day, this should be decided on a case-by-case basis with an application and a school report indicating how the additional time will enrich the quality of the educational experience. Additional funding should be provided only after the report has been read and approved of, confirming the merit of the additional time.