Do not put your dslr in a handlebar bag.
Best versatile way I've found to carry a simple setup (dslr, one long, one short lens, and monopod) is to get the smallest lowepro that will fit what you need (ridgerunner is one of the ones I use) and then put it in your pack with whatever you can pad it with.
I've got a full camera pack that I'll carry of a real shoot, or for videography, but then I dont' have my ABS pack or avy gear... which isn't the way I like to do things. Just bought an ABS vario (with a 15L & 50L attachment) so that I'll have more room to carry a full complement of gear on a shoot & still have a full avy pack.
Another one that works well is the microtrekker, once you upgrade to a 70-200 (f4 of 2.8) it'll still fit along with a wide & one flash, but it normally will fit inside of most decent sized bags.
If you're willing to bastard up your tunnel, I'd say go the peli route though, that's the safest, and if you've got it outfitted properly, I wouldn't worry AT ALL about vibration being an issue, we've done MUCH worse with peli cases.
I'm just not willing to put more crap on my sled.