For some time I have done my best to run like motive power together, all NYC, PRR, etc, thinking I was doing the right thing.
Today, at my daughter's soccer game, which has a very busy rail line behind it, I saw a wonderful intermodal train, being pulled by a BNSF, CSX, and NS engines. This was followed by a mixed freight lead by a UP and NS pair.
From here out it is whatever I choice, seemingly just like the real railroads do it.
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Ahhh Jason, you are no longer a purist I take it. Your are a bold man my friend. 
I must admit that I am still a purist in terms of running matching engines and passenger cars. Maybe it is the fact that I am just too old to change.
Jason my Friend...you have "graduated"!!! Being a fan of the same roads you listed in your post above, I for years kept motive power of the same road name together and on separate trains....but haven't done so for years! In the prototype, this may be more common when one gets within the main part or interior of a particular railroad's system but as you have now found out, sometimes railroads share "trains" and motive power...especially near areas where they interchange or service the same industries, etc.
While I generally keep my passenger trains within their respective motive power road names, I do mix the more modern freight diesel road names that mimic their real world prototypes. Right now I have a 36 car unit train made up of Atlas articulated as well as the new Lionel auto carriers headed up by two NS units and one UP unit! I enjoy the unit trains as they remind me of the freight version of a passenger train!! The Twin Lakes Central is a freight as well as passenger train railroad and has quite a few different road names since the layout represents a somewhat fictional midwestern city....
Alan
Jason:
Thank goodness that this decision does not effect your passenger train operations. I was ready to go to the pharmacist to get some sleeping pills so that I could sleep tonight. I even had the car warming up. WOW, I am so relieved. 
Wandering motive power is practically routine these days. I caught a glimpse the other day of a train entering BNSF's Eola yard with CSX and KCS power on the point.
The NS has been pretty popular on the BNSF also, as seen in this 2002 picture:
Back in the day, I can recall GN FTs being lead out of Clyde (Cicero) by a Burlington F-unit and some NYC or UP locomotives spliced between two Burlington units.
Rusty
So triple heading a mixed freight/passenger train with a UP Big Boy, Chessie Gp38-2, and a PRR GG1 with an Amtrak HHP-8 as helper isn't normal?
In defense of those who love matched motive power and cars, the final train I saw was headed by a pair of CSX matched units, followed by a bazillion tan CSX hoppers. It was the most uninteresting train of the afternoon.
The most interesting had no two like cars, it was like someone thought it would be fun to take one of everything in the yard and hook them together.
As the self-appointed Information Minister of the Isle of Denial, I must say that mixed motive power is the gateway drug of merger mania!
OK, now that I've made my "official" statement I see it quite frequently running out of San Bernardino towards Cajon. I don't know if it's borrowed/leased motive power or through units handed off with a train making return trips home, but it does happen. So doing the same in a model context makes perfect sense to me.
As for passenger service, you did see the occasional through sleeper or coach being handed off from one road to another, so that works pre-Amtrak. Post Amtrak, it's called an excursion and anything goes.
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