There are exceptions, certainly in colloquial speech variants, 雰囲気 and 原因 come to mind. Both have an annoying ん ("n") in the middle that makes them a pain to pronounce even for natives, so the first gets changed from ふんいき to ふいんき and the latter from げんいん to げいいん. So, if written properly in hiragana you'd know how to pronounce them "properly" but not necessarily as they're actually used by a significant amount of people when spoken. Even the auto-kanji-conversion of my keyboard respects the variants.