Technically speaking, "damage [...] is reduced by 3" is neither Resistance nor Immunity, so it doesn't get overcome by a monk's fists.
That said, player-side effects like these don't often come into contact. It's certainly possible for two PCs to get into a fight where this matters, most often due to confusion, domination, etc., but ending up with this particular pair of abilities in conflict is the edgiest of edge cases. Monsters almost always use basic Resistance for this purpose. While I can't guarantee there's no enemy or spell anywhere that gives nonstandard damage reduction, I haven't seen it.
Because of that, as a DM, I can't see any balance issues with taking a broader reading that monk unarmed strikes just count as magic weapons any time it matters to an attack. I would not get too hung up on the exact text. It's never fun to tell your players "no, that doesn't work", especially when they seem at first glance to have a class ability that's specifically made for the situation at hand.
Normally, restrictive rules can be traced to one of two sources: a restriction to enforce game balance (such as, say, the rule about only being able to cast a cantrip at the same times as a bonus action spell), or a restriction to enforce the flavor of a specific ability (such as sneak attack being limited to small, quick weapons). Since this doesn't appear to do either, I'm left to wonder why it would be written this way. I suspect this is one of those situations where "helper text" accidentally made the ability more limited than it was meant to be. If the monk's ability simply said "the monk's fists count as magic weapons", that could immediately make your player ask "What does that mean? Why do I care?" (or worse, start thinking their unarmed strikes are innate +1 weapons), so I think they put in text that clarifies the benefit that magic unarmed strikes bring -- and it covers 98% of situations, but incidentally excludes a couple of weird corner cases that it maybe shouldn't.