Yes, Starfleet also uses the term Commander-in-Chief for its highest ranking officer, which seems really sloppy.
Is it the highest-ranking officer for sure? I remember one in ST6, but hasn't there also been a Starfleet Chief of Staff somewhere? "Chief of staff" seems more in line with modern ideas of high-level command and control.
As for sloppiness... In US history the navy had fleet commanders-in-chief since the early 1900s. Post WW2 the title was extended to Army (CINCUSAEUR) and Air Force (CINCSAC) commanders. Eventually it became the standard title for unified combatant commanders. Nobody confused them with the president. Even so, in 2002 Secretary of Defense Donald Rumsfeld decided that only the president should have that title, and all the uniformed CinC's dropped the "in chief."
In WW2 the US Navy had the CinC US Fleet, CinC Pacific Fleet and CinC Atlantic Fleet. One day as FDR was gearing up to run for reelection in 1944, his military chief of staff Admiral Leahy approached the CinC US Fleet, Admiral King. King could be, let's say, not an easy person to deal with. Admiral Leahy said that the president would like the navy CinC's to drop the "in chief" from their titles. King thought this was political, to emphasize that the president was running the war. He said fine, when the president issues an order to that effect, I will do it. Leahy said the president did not want to issue an order, but would just like it to be done. King said, well, I personally see no reason to do that, and that was the end of it!
E.J. King and W.M. Whitehill, Fleet Admiral King: A Naval Record, 1952.
E.J. King and W.M. Whitehill, Fleet Admiral King: A Naval Record, 1952.
The British Royal Navy used the commander-in-chief title for fleet and major base commanders for hundreds of years. In WW2 they had CinC Portsmouth, CinC Plymouth, CinC the Nore, CinC Rosyth, CinC Western Approaches, CinC Home Fleet, CinC Mediterranean, CinC South Atlantic, CinC East Indies, CinC British Pacific Fleet and probably some I'm forgetting. I think the last RN CinC positions (CinC Fleet, CinC Home) were disestablished about 10 years ago.