The Death of Imagination

It's not a matter of kun'yomi vs. on'yomi but of an ateji pronunciation. An on'yomi for 百日紅 would be something like *hyakunichikou (cf. sennichikou for 千日紅 "globe amaranth"); a theoretical kun'yomi is harder to come up with--hyakuhibeni? The point is that neither of these pronunciations is ever used. That these three characters together are arbitrarily pronounced sarusurebi is just something you memorise when you learn Japanese, like the fact that 河童 is kappa or 大人 is otona.