I used the Genki books which also use Hepburn. Simply put Hepburn mimics the English language and, the English language uses apostrophes for glottal stops. Especially if the language foreign. This is why Genki does that.
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").