It could be his poops hat are smelly. Even neutered buns can have strong smelling poop. It’s then a strong onion-like odour.

Have you checked his anal glands? They can become plugged up. Here is a nice video on how to clean them: https://youtu.be/_x9dbSUdomg

Some rabbitfoods have odour-reducing components, most commonly yucca schidigera.

Pee on hay could potentially cause odor, because even though urine is normally sterile when it leaves the body, it contains nutrients that bacteria normally present on hay could use as food.

Is he peeing a normal amount you think? Concentrated urine would smell more. Have you seen him strain to pee?

Part of me wonders if maybe he just peed in a specific area of the box that day, so the urine kind of built up more than normal in one area?

I’ve also heard that sometimes additional protein in the diet can cause urine to smell more strongly because more urea is produced, but I need to find the primary source on that (and I might have my mechanism slightly wrong). I think I recall you increased his pellets recently? Maybe that could have something to do with it?

Increase in protein would result in more urea because the nitrogen in the aminoacids is shed in the urine in the form of urea. So an increase in protein intake would cause smellier urine.