Sometimes padding can help. That padding could come in the form of rolled washcloths on either side of the tube to create a gap for the tube. A member here has a Nautilus crotch pad on her Frontier because that's what her tubie needs.
Neither of those are approved "fixes." Officially you never add anything to the seat, don't use aftermarket padding, and don't put anything other than regular clothes between the child and the harness. In a special needs situation, you start bending the rules as little as possible to accommodate the child's needs while not compromising the child's safety.