"What they want are students who understand the principles of research."
But the same still applies. You have to show that they actually aren't teaching such principles, not just that their conclusions are different.
You are still missing the difference between _teaching/understanding_ and _believing_. The former is required, but to require the latter is viewpoint discrimination.
If the students didn't know the methodologies and assumptions, that would be problematic. If they didn't understand the principles of research, that would also be problematic. However, if they knew of different principles IN ADDITION TO the other ones, then it is truly viewpoint discrimination to penalize them.
If someone knows all of the data, understands the principles, and is even able to apply them, yet disagrees, and they are forced into remedial theory until they "believe correctly", that is called BRAINWASHING.
I tend to agree that individuals who perform well and demonsrate their knowledge should get credit for their achievement and not be penalized because of their school.
If you can earn college credit by taking a test, you should be able to demonstrate objectively that your high school credits are valid.
This does not contradict my belief that science is an activity rather than a list of facts.