I disagree. My natural inclination would be to not say anything, for fear of adding to this person's distress.
But firstly, that's how we got into this mess in the first place.
Secondly, and more importantly, this is not, and never has been, about individuals.
There is no room in the ideology to make a distinction between a nice guy and a bad guy. If there was, I would fully support it.
The fact that this chap is nice, should absolutely determine the way you approach it, though.
Which is why I asked if there are gender neutral facilities.
Offering a gender neutral facility will often solve the issue. If they are happy to use it, which many are, problem solved.
If they are not, it will highlight why. At which point, HR absolutely need to be alerted to those reasons.
Because they need to deal with it. They need to address the issue.
That may HR accepts that this person has every intention of using the women's facilities, despite any objection. Which they may well end up agreeing to (HR I mean).
But pretending there is no process to go through, no objections to acknowledge, and no conclusion to draw is what is happening everywhere.