The best answer is supply and demand. Right now there is not much of a need for so many lease locomotives out there. There are a lot of fully functional locomotives out there that are just parked in rows waiting to be needed again. So for BUGX there is no point in paying to move those locomotives that need work or a full rebuild in some of those cases you listed. Spend more money on them getting them ready to lease then have no one want to pay to use them. So right now it is best to just let them sit until they are needed. Yes some will probably end up as parts for other locomotives in the fleet. I am with you I would love to see a lot of those locomotives that are on the NWP go back into service but until there is a need the business has to make ends meet so there is no point in spending money on something that will just keep sitting.

The locomotives in Willits can currently only be trucked out. Good luck getting road permits to do that.
Same with the ones in Eureka. If I remember right BUGX owns the 4 GP units that are left up there. The one that NCRA owned got scrapped last year. As long as steel prices remain low they will survive longer although they are right next to salty air so time will also not be good for them either.
The SD9 in Turlock got a full rebuild I think 5 years ago and new paint. I don't know if it ever got leased or not since about that time is when the locomotive leasing industry started slowing down.