lcayton, I can't comment on the racks or how to avoid hurting your bike because I don't know them - have never seen a bus rack of any type actually.
I understand what you're saying about wanting to ride your nice bike on the way home too.
Then we need to factor in that commuting at any level is really hard on the bike, much harder than any type of competition.
Sooooo, how about this for a thought -
Build yourself a commuter but build it as a completely different style of bike such as a fixed gear bike. Something sporty and fun, something different so you're not comparing it with your good bike and something to give you a different experience - let's face it, as experiences go, commuting is right up there with root canal work.
It doesn't have to be expensive - better if it's not, and that's where the fixed gear bike makes some manic sense because all you need is an old roadie and convert it with some track bits, but you could do the same with a mountain bike (there you go, build a fixed mtb

) or a SS bush basher or ... It doesn't matter, just something that'll do the commute, won't complain about the inevitable damage and which still gets you smiling when you ride it. Then you'll be able to put a carbon form back on your good bike.
Richard