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Yeah, the MDS Moriwaki or whatever it was that raced in the Japanese series had a CRF based engine. I can't recall whether they ever made it to Moto3 WC
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The Moriwaki MD250 uses the CRF Honda engine and NSF chassis. They are in a few Moto3 champs around the world, don't think anyone has one in Moto3 WC, but you can buy one from Ten Kate for 11k euros.
I see that the Dutch GP3 champs will lease you an MD for 6k euros for the season - damned good price to get into GP-class racing.