I've run some partial transparency before. Psionics and Magic do not affect each other but certain creature types had a built in psionic resistance. If a creature had SR, the creature also had PR equal to half the SR + a racial bonus. The racial bonus was different based on the creature time. For example dragons and aberrations might have a +8 racial bonus to PR but a magical creature might only have a +4. The idea was that alien minds are far harder to affect than humanoid minds. I had little problem maintaining psionic vs magic. Most of the creatures were in the magic sphere but I threw in some psionic monsters to make my player's psychic warrior feel special.
Psionics in my game was rare. Psions were seen as godless monsters by the public, but secretly the world governments employed psions as bodyguards, seers, or to construct psionic defenses.