It's a pretty subtle point, but the author is saying that "some words were originally written in kanji", while I'm noting that for a word like ここ, that's only true if you include the time when
everything was originally written kanji. So the statement is technically correct, but IMHO rather misleading, since (the man'yogana pre-kana period aside) it's generally quite rare for word to make the leap from kanji to kana.
An even more subtle point is that kanji usage is fluid, so it's perfectly correct to write many words as kanji or kana, but with subtle shifts in meaning. For example, いい and 良い are both "good", but the latter is more formal and may even be read differently (yoi vs ii).
