I can't say what the CAPTE requirements are, but it is quite possible that those clinical education and PTs as learners and educators courses are required for accreditation and your school is giving you the minimum number of hours they can. What I'm saying is this may be outside of your school's control.
In regards to the 3 research methods courses - yes. 3 are necessary. They will be some of the most important courses you will take as a PT student. They are what will help you shape your practice as a new graduate and then modify it as you gain experience, using new and relevant research that you have critically appraised. From my experience, these are some of the courses that my students tend to complain about, yet all of them seem to think that evidenced based practice is important. If one can't appropriately critically appraise the current literature, how then are they able to practice in an evidenced based fashion? The simple answer is, they can't. They then tend to fall back on the traditional memes in taught in PT school or continuing education courses, or use reasoning like "This is something my CI showed me.", etc., which frankly, is not the way a professional should behave and does your patients a considerable disservice.