What’s so confusing about the fact that word roots are pointless if they don’t point to how a word is supposed to be used?
Suppose I was inventing a word, let’s say “chronocide”, and someone asked “if ‘chrono’ means ‘time’ and ‘cide’ means ‘to kill’, does ‘chronocide’ mean to kill some time” only for me to say “no, it’s a name I gave a new state of matter”, would that not be a waste of word construction?
The word wouldn’t be applied to that for long though, as inevitably people going by the same train of thought as the other person might one day look for a fancy word that means “to kill some time”, and the meaning of “chronocide” would slowly shift to its most fitting meaning.
Etymology has jurisdictional overwriting power over popularly-given word meanings for the very reason that it contains multiple words (in other languages no less) that already have an established meaning that would have to change first and simultaneously.