“Whether there was any incidental effect on intrastate commerce was irrelevant”
You have it backwards here, and I’ll tell you why. It’s not that the law had a sideffect on intrastate commerce. The feds wanted to control prices on interstate commerce but realized that the railroads got around this by charging different rates for travel within the states. So in furtherance of the goal of controlling interstate rates they extended their power to apply to intrastate rates. This was not “incidental;” it was a deliberate extension of power to a realm it had been in before (though it was inspired in my opinion by Gibbons, as I said).
Now not only would interstate commerce be regulatable, but commerce that directly affected interstate commerce would be, too. It’s a hop and not even a skip and a jump from there to non-commercial activity which substantially affects interstate commerce being regulatable. Wickard didn’t turn the Shreveport Rate Cases upsidedown; it merely extended the logic a bit.
Them being registered federal carriers is a red herring, by the way. Just because they carry passengers and freight across state lines does nit mean you write whatever laws you want covering their intrastate activities. You couldn’t have, for instance, mandated they offer so and so dollars an hour to their employees any more than you can order them to charge a certain rate on intrastate lines.
Notice how cleverly your bold faced quote specifies how “necessary” regulating rates on lines substantially relating to interstate lines is to the interstate regulatory scheme as a whole. Perhaps, but then again what if the regulatory scheme they have in mind is unconstitutional? Regulating prices intrastate is not necessary to regulate prices interstate. Regulating prices intrastate may be necessary to regulate interstate trips the whole way. But who said the feds can do that?
The arguments in support of the claim of federal authority to act hinges on the status of the railroad as a registered carrier of interstate commerce. Without that, their entire arguemnt falls apart. Roscoe Filburn was not a registered carrier of interstate commerce.