SEA 737,
In the past, I received many rides from your colleagues between SEA and ORD to commute for my RJ job. I often rode on the flight deck, and even during times when tensions were highest between UAL and UAX crews, I was treated with respect and professionalism. For that I have always been grateful.
More than once, when riding in the back under OMC authority, I had a captain tell me that if I was assigned a seat in the back I didn't need to check in with him/her. I followed this advise exactly once: I ended up receiving a verbal lashing from an A319 captain just before the red-eye pushed back at the N concourse. But I made it to work.
Since then I always checked in with the captain, and was happy to do it. And I often watched as other OMC riders didn't even look the way of the flight deck before proceeding down the isle to their middle seat. Sometimes they were regional pilots, but plenty of these folks were mainline too. AA, AS, heavy freight drivers. I never saw them singled out for not "checking in"...
I agree with you: OMC riders should always check in with the flight deck. Riding as a jump seater - in the back or up front - is a privilege, and at the captain's pleasure. Although I've since handed off my RJ job (and jump seat rides) to guys who are younger and more ambitious about a flying career than myself, I thought you might enjoy this perspective.