While I can still touch my toes, I never was able to get to a full split, despite almost daily stretching, yet, like you, was able to accurately kick to the head. I am certain my pelvis was not constructed to do splits, but then how the head kicks? Perhaps muscle powered momentum, along with relaxation and proper technique were responsible.
Anyway, for me the question is moot as head kicks are no longer part of my bag of tools. No great loss though, as my other tools and technique are well able to compensate. Must admit that head kicks are useful in tournament competition to help spread out the opponent's defense (much like an occasional long pass in football) but not essential for non-TKD bouts.