EzekielRaiden
Follower of the Way
The monk uses a d6 for their short sword the d4 relates to the Bonus unarmed strike which would be a d4 + Dex
Short swords are monk weapons, so this feature potentially applies to them as well.
In general, I am against the ambiguity of "can" vs. "must"/"should," because it usually makes things more confusing. This is an unusual case where that doesn't apply; they very appropriately used "can" instead of a more binding term, to allow for such situations where it would actually be an illogical detriment. Eventually, your monk die will be better than the short sword's d6, at which point you'll surely use the monk die instead.