When creating a modulator at the preset level that has source/destination/curve identical to a default modulator, Polyphone will report the modulator to be "overriding default mod" or "disabling default mod." However, only instrument-level modulators can disable or override a default modulator. Preset-level modulators work independently, adding to whatever happens at the instrument level.
This oversight only appears to affect modulator labeling, as Polyphone's synth engine seems to be calculating things correctly.