Yeah, that's my plan if I get hassled- just rotate the bars and the stem so everything fits in spec. And deflate my tires if that extra inch of length is just going to kill them.
Although after asking around, it doesn't sound like it's a big deal. I probably wouldn't be able to get away with taking my Big Dummy, but anything that resembles a normal bicycle is fine. They'll even accommodate bikes that don't quite fit in the onboard racks.