JI Guy, STOP IT! What are you, three years old?
Forget about the DOT and frequent flyer programs for a moment. Let me explain how this works from the perspective of pricing an airline ticket. Given the huge variance in fares and the increasing number of people who book their own tickets, I think this is an important point.
There are several fares available in the PDX-PHL market. You can buy a ticket from DL, AA, NW, CO, HP, UA or US. With 6 of those 7 airlines (any but US), you can choose plain old non-codeshare flights the whole way. You can fly DL PDX-ATL-PHL, you can fly AA PDX-DFW-PHL, you can fly NW PDX-MSP-PHL, you can fly CO PDX-IAH-PHL, you can fly HP PDX-PHX-PHL, and you can fly UA PDX-DEN-PHL.
If you choose to buy the ticket from US, you have no choice but to fly on a flight operated by UA from PDX to DEN since US operates no flights at all out of PDX.
Now let's consider this possibility -- go to Expedia.com or Travelocity.com or whatever, and choose "multiple cities". Enter PDX to DEN, DEN to PHL, PHL to DEN and DEN to PDX. Leave airline choice as "any airline".
Choose a plain old UA flight from PDX to DEN, and a plain old US flight DEN to PHL, and the same for the return flights.
The resulting fare you see will probably be greater than the fare you paid (if DEN is on sale, and the fare is less this way, that's a pretty obvious solution).
Why is this? By choosing a UA flight number from PDX to DEN and a US flight number from DEN to PHL, the fare quote you get back is PDX-DEN roundtrip plus DEN-PHL roundtrip. You have essentially created a PDX to PHL roundtrip with a DEN stopover in both directions (not connection, a stopover). Because it's actually two different fares, you can make your DEN stopover any length of time you want -- 45 minutes or 8 months, your choice.
The only way to get a roundtrip fare from PDX to PHL is to have just one airline code for all of the flights. It doesn't matter who operates them.