They are also smaller areas with basically no population. Think about it, Ordona Province has Ordon Woods and Ordon Village. The Faron Province may not necessarily have a village, but it's an important area that must be passed through to reach Ordon, PLUS it has the Forest Temple and a large population of monkeys. Eldin Province has Kakiriko Village and the Goron Tribe. Lanayru Province, of course, has Castle Town and Zora's Domain. But the Peak Province really just has Yeto and Yeta. No one really ever goes there, and no one even needs to pass through there. And the Desert Province has been fully shut off from access by Hylians (except for if Fyer launches them over there, and then how can they get back without Midna's warping ability, which was the only reason Link could get back), and absolutely no one lives there save for the Sages.
So the light spirits seem to inhabit locations of high population density OR places that are often passed through or visited.