To answer your second question first, you are corect that if the flight is not purchased as an AS marketed AS numbered flight then you would be waiting until after you get to the airport to be put on the upgrade waitlist. As far as advance MVP seating, YMMV.

As fare a being able to book the flight as a codeshare thats a little tougher. First of all not all AS flights are codeshared with another partner. Second, not all codeshared flights are available as "stand alone" codeshares. For example, AS137 is codeshared with DL. If you go to DL.com and price an itinerary from SLC-ANC you'll see the AS flight listed as DL9073 after the DL operated flight from SLC to PDX. If you're just going from PDX-ANC, however, there is no way to book AS137 alone as DL9073. The codeshare totally depends on the connecting flight.

There are some "stand-alone" codeshares. For instance PHX-SEA. Almost all of the AS non-stops are available on AA.com under the AA codeshare flight number and usually the fares are lower as well. It all depends on the route and which partner is doing the codesharing.