I have heard that some freight railways are OK with Amtrak having their own tracks built on the existing right of ways, tho I am not sure what sort of compensation might be envisioned.
We're doing that in Washington State right now, and we're in the environmental impact phases of it. The state DOT is paying the BNSF to build a 110 mph third track for 20 miles that would be dedicated to our Cascades Service passenger trains owned by the state DOT and operated by Amtrak under contract.
The general rule is that the BNSF will gladly build you anything you want -- as long as you pay for it.