I think you have a very warped idea of how Hepburn works and your confusion is just caused by not knowing Hepburn. You would probably be better off actually loo

I think you have a very warped idea of how Hepburn works and your confusion is just caused by not knowing Hepburn. You would probably be better off actually looking up the rules of Hepburn instead of assuming that it's just the English language. The Genki books seem to not use apostrophe but a dash, since I found a PDF of it and it uses the terms "on-yomi" and "kun-yomi" to distinguish んよ (n'yo / n-yo) and にょ (nyo). It also very clearly says that った becomes "tta" right in the beginning, so I have no idea where your apostrophe usage comes from. 港南 has a very unambiguous Hepburn romanisation of kōnan, which is impossible to confuse for こなん ("konan") or こんあん ("kon'an" / "kon-an").