Star Trek

Strictly speaking, O'Brien is a "Senior Chief Petty Officer" in rank, and a "transporter chief" in role. Those two happen to both include the word "chief", but they're no more related than "Lieutenant Commander" and "chief engineering officer" are for La Forge. I believe "chief", on its own, is referring to any of the ranks of NCO with chief in the title, [master | senior] chief petty officer.

Starfleet seems ridiculously officer heavy

Indeed it does. Whether this is actually true, or just an artifact of the fact that we tend to primarily watch the actions of those in command, I'm not sure. But if it is the in-universe reality, that's probably a consequence of the post-scarcity society and the abundance of time and education people have in order to become officers.

And where are all the warrant officers?

I'm gonna be honest, I've tried numerous times, but have never managed to really understand what WOs are. I have this vague sense that their rank sits somewhere between that of NCOs and of commissioned officers, and that they're involved in more unusual or specialised tasks, but I don't think they normally sit in a regular chain of command, and I'm not really sure how it works.