Let me simplify it for you.

It's pronounced kernel because there were originally two ways to say and spell it. Colonello (The Italian translation) and coronel (The Spanish translation). Like most words, overtime it evolved and the the pronunciation changed and became mixed in a way which makes it sound like ˈkəːn(ə)l. The spelling of the word also evolved, it became spelt like the Spanish translation, coronel but with the L from the Italian spelling to make Colonel.

Words evolve, just look at old English and compare it to now. It's very different but you can see how certain words are similar to how we would say them today.