C&NW/UP and Metra

Why did the Chicago & Northwestern continue to operate their commuter trains into the RTA era?

It is my understanding that, to this day, Metra trains on the 3 ex-C&NW lines are still crewed and run by Union Pacific, with only the equipment coming from Metra itself.

If I'm not mistaken, the BNSF has a similar arrangement.

At the beginning of the RTA, all of the commuter railroads had purchase of service agreements under which they continued to operate the trains with deficits covered by the RTA. With the bankruptcy of the Rock Island and Milwaukee Road, the RTA/Metra purchased those routes and the employees became RTA/Metra employees. Metra purchased the IC electric lines when that railroad was on a selling spree. At the same time, Metra gained operating rights over the ex-GM&O routes. The N&W/ex-Wabash route became Metra's when the public agency leased the line as part of a service expansion. The North Central line originated as a Metra project. Meanwhile, UP and BNSF continued to operate under the purchase of service agreements which seems OK with everybody, so there was no need to change the operating accords.