Natural languages have an element of chaos, if you ask me:
'“Colonel” is pronounced just like “kernel.” How did this happen? From borrowing the same word from two different places. In the 1500s, English borrowed a bunch of military vocabulary from French, words like cavalerie, infanterie, citadelle, canon, and also, coronel. The French had borrowed them from the Italians, then the reigning experts in the art of war, but in doing so, had changed colonello to coronel.'
The way that we spell colonel,
can be explained by history.
English spelling is infernal,
but needn't be a mystery.