I had to chuckle. I have a preschool and see all sorts of clothes come in and out of my school.
Here's my question to you, teacher to teacher: can you let it go? Is it worth the conversation with the parent? Some kids really don't like various clothing items: socks is a great example. What if the mom does know, and just doesn't care?
I have to tell you, honestly, that if my son was dead-set on not wearing underpants, I'd really be okay with it. Personally, if it were me, unless there was a total hygiene issue (coming to school in the same pants with racing stripes), this is a conversation I would avoid having. I am really very careful about making things "rules" with parents unless it's absolutely unavoidable or a hard line I need to take. Right now, in my group, my 'rules' for parents are that no sweets come to school in lunchboxes and that all the children are appropriately dressed for outdoor play for this current weather. I believe in letting my families allow their children to otherwise let them dress themselves. When we challenge a parent's usual practices with our own rules, we do often run the risk of offending. So, unless you are seeing significant red flags (child is dirty, hair never brushed, etc.), this is an area I'd encourage you to let go of. Eventually, the child will become more aware that all their peers wear underpants...or they will graduate to middle school/junior high, where there are requirements for dress.
Try to stay zen with this one. Over the years, I've had my challenges too! We bend, but we won't break, ha ha. The trick with all of childcare is to stay as flexible as possible. (and you can always just ask the child "Oh, I noticed that you don't usually wear underwear to school. Tell me about that." Do it when you have a moment alone with him, and see what he says. He might just hate underwear!:) )