As per Phil law you are required to register your extra barrel. It's really up to you if you want to do it, lots of shooters doesn't bother to.
Are you more concern of the competition or what the law requires? If I were the RO I'd notice your bullet hole but I'm not familiar with IPSC ruling. But if you're shooting IDPA I'll let you get away with it since we're just having fun.
To stay out of trouble with the law just put the 45 upper when you're traveling like mc_o said.
Niner # 558