Some historical makura kotoba have developed into the usual words for their meaning in modern Japanese, replacing the terms they originally alluded to. For example, niwa tsu tori (庭つ鳥, bird of the garden) was in classical Japanese a makura kotoba for kake (鶏, chicken). In modern Japanese, niwatori has displaced the latter word outright and become the everyday word for "chicken" (dropping the case marker tsu along the way).
That gave me a "now it all makes sense!" moment, as "niwatori" had always struck me as slightly odd.
I feel there must be quite a few words in English where a poetic term has replaced the ordinary one, or at least because as common, but I'm having trouble coming up with them. "Robin" for "redbreast" by way of "robin redbreast" is one, I suppose, and you can trace a similar route for some rhyming slang: it only occurred to me the other day that "Use your loaf!" involved rhyming slang, for example. But surely there must be other/better examples?