For background, the question appears to be about the purchase announced by Metra on February 21, 2018: [www.metrarail.com
Looking at Wikipedia (https://en.wikipedia.org/wiki/Siemens_Charger
), the numbers are suspicious: 22 Chargers are going to Calif. while 21 F59PHIs are going from the "west coast" to Chicago. However, "west coast" could also include the Cascades service in the PacNW which also uses F59PHIs. Some of the Calif. units have in fact been rebuilt in recent years; not sure about Cascades. Other than paint job, there's no difference between Surfliner and other Cal-Amtrak units, and they're all owned by the state, so if California is the source (or a source) of the units going to Metra then they're being sold by the state not the Surfliner JPA.
I'm slightly surprised that they're being sold, especially recent rebuilds. Cal-Amtrak is chronically short of locomotives & rolling stock - running with few spares. Lack of equipment is a common reason for not adding service in all 3 corridors. I would think that keeping the F59PHIs would be preferable to leasing old Amtrak GE units. But I don't run the Rail Division.
As for comparison to the F40s - that does sound a little bogus. Yes, both models came from EMD. But the F40s (unless extensively rebuilt) are very simple, old locomotives. The F59PHIs are newer, emission-controlled locomotives (pioneered electronic fuel injection in the EMD line), and almost certainly will throw the shop staff a few curves. And the F59PHI uses a separate genset for HEP - iirc from Wiki and magazine articles, Metra's other stuff mostly uses direct-drive HEP, so that's another potential headache (anything different is a potential headache) for the shop staff. In all, they're similar to the F40s mainly in who built them.