BNSF is much more transparent and straightforward than most of the other Class Is. UP doesn't publish their PTC status in detail, though rumor has it that over half is done. Last I read, there is NO working PTC on NS, CSX, or CN. Not sure about CP.
I continue to assert that BNSF has no particular interest in having Amtrak run on a route which they barely use any more, want to get rid of, but are somehow still stuck owning.
I'm pretty sure they would happily move Amtrak over to the Southern Transcon once it's double-tracked (and with appropriate standards for station design, as I said, passenger sidings and platforms on both sides, and of course funding for the trackwork at Belen and so forth).
I don't think "we might want Denver-Albuqerque service eventually, so we need to keep running a train over Raton Pass" is a good argument for hobbling the Southwest Chief. If we actually had some sort of movement towards Denver-Albuquerque service, that would be different, but we don't. Colorado can't even be convinced to run service from Denver to Fort Collins, and this is with a relatively pro-public-transport administration. Out of state service is something they won't even look at.
There is currently a PTC waiver for routes with a "de minimis" number of passenger trains per day. I don't know how long that's going to last, but it's not a good thing to rely on; that sort of waiver has a tendency to shrink over time.