I am a biomedical engineer and the best part about what counts in your sciGPA and what doesn't is up to you. When you fill out your AMCAS you designate which is which and for many of my bioengineering classes I either classified them as biology, chemistry, or physics. For example, my heat and mass transfer class was a differential equations based physics class, so I put that down as physics on my AMCAS (also because I got an A in it). I got a B in bioelectronics (which I could have classified as physics), but I didn't include that in my BCPM GPA and the AAMC didn't give two ****s. I think you largely have control over what you choose is BCPM and what isn't but remember they can change whatever they want once you submit it for verification (they didn't for me).
As for the classes you listed here are what I classified them under (as I took either the exact same class or an analogous class with a different name):
Human Physiology for Engineers - BIOLOGY
Biophysics (in the engineering) - PHYSICS
Biomolecular Engineering - CHEMISTRY
Biomaterials - CHEMISTRY
Systems Physiology - I couldn't classify this as any so I kept it as an engineering course
Functional Anatomy - BIOLOGY
And anymore, just list them..
I guess another good rule of thumb is to just think it through as you're taking the class. I remember for my Molecular Physical Chemistry class I thought it would be very rigorous math-based physically-oriented class but it turned out to be more chemical theory than I thought, so I classified it as chemistry and AMCAS approved of it.
Bottom line: you have a lot of leeway as a biomedical engineer so feel free to classify as you wish because AMCAS probably won't question it (they won't have time to). Also good luck buddy, so far all the schools I have interviewed at just love biomedical engineers. Ace the MCAT and you are set.