Also, why does cause and effect being important (and I agree with you there) reduce the importance of philosophy in science?
To me, the rethinking of what is meant by space and time in relativity, and what is meant by measurement in quantum physics are both extremely philosophical...and yet still shed light on cause and effect.
Perhaps, I am naive about what is possible. But you yourself said that ab initio calculations tend to give the best results. I think it is important to reflect on why that is, and to know what it is you are giving up as you go further away from these sort of calculations.
A couple of statements in the link you gave stood out to me.
"Although most chemists avoid the true paper & pencil type of theoretical chemistry, keep in mind that this is what many Nobel prizes have been awarded for."
"What approximations are being made? Which are significant? This is how you avoid looking like a complete fool, when you successfully perform a calculation that is complete garbage. An example would be trying to find out about vibrational motions that are very anharmonic, when the calculation uses a harmonic oscillator approximation."
Frankly, the "How to do a computational research project" section in the link read as being fairly philosophical.