This especially is extremely confusing. Aside from historical considerations (focus on orthodoxy benefiting the spread of new ideas? Enforcing jizya boosting recruitment? Akbar the Great favoring legalism?), there are obvious gameplay discrepancies. Attacking countries of your own religion gives you mysticism points and missionary bonuses, which you don't need in the provinces you just conquered. On the contrary, when you actually convert provinces you drift toward legalism and your missionaries become worse.
And ideas. Now the religious group synergies with mysticism, but it gives you a permanent casus belli against infidels, which instead promotes legalism. It's even stated on the DLC banner, "attitude toward innovation and syncretism": and yet syncretism and innovation are opposite in-game. For the life of me, I can't see any sense in this.