Gapped-scale tunes seem to predate harmony in the European folk traditions, and the great majority of them are used for songs that never got harmonized. I don't believe many gapped tunes are derived from heptatonic antecedents.

The "phrygian-sounding" flamenco music is mostly in hijaz (the third is sharpened as in the major scale). True phrygian doesn't seem quite as common, though it's more common than in the British Isles.

Lydian seems to be most common in Scandinavia - it's not all that usual in eastern Europe (if the fourth is sharpened, it's more often in a scale with a minor third, like nikriz or misheberekh). I would guess that the Scottish examples are mainly of Norse origin.