Protection vs Alignment and Magic Circle vs Alignment have no effect on the caster (this include the drinker of a potion or the user of a scroll or item). All they do is:
1) Prevent summoned creatures (of any type or alignment) from physically contacting the subject, or crossing through the circle.
2) Provides additional protection against the attacks from creatures of the warded alignment in the form of +2 deflection to AC and +2 resistance to saves.
3) Suppresses ongoing compulsions for the duration of the spell, regardless of alignment of the caster of the compulsion.
So no, Caerwyn being chaotic in alignment would not hurt him when using protection spells vs chaos.