Colleges do take into account what is offered at your school but it’s still tough when you are competing with students who have taken MVC, physics C, etc… State flagships typically are more apt to waive those things for their instate applicants if they weren’t offered. A tougher sell at CMU, Mudd, etc…
The other red flag to me is no third year of Foreign Language. Many of the competitive schools require 3 years and prefer 4.