I would also suggest changing out the toilet seat if you haven’t. We have had to do that at times b/c even when they look clean, sometimes they are stained with urine and you just can’t get the smell out b/c it gets in the hinges and such.
As for the culprit(s), I will say as a Momma of 4 sons, their bathroom upstairs (that they solely use except on rare occasion we have guests), does SMELL until they clean it each week. I don’t allow them to urinate outside the toilet bowl but apparently it just happens. If I catch anyone being sloppy, they must clean it right then. My little girls’ bathroom which DD1 uses only (DD2 still in diapers), it never smells. I do think boys are harder on bathrooms than girls.
I would second checking the seal and also try changing the toilet seat.