This discussion points out that "change" is cumulative. When somebody borrowed switches and rail from west of the Chama wye, it's likely nobody thought it was a problem, especially if it was to build the leads to the new enginehouse. Later on the warehouse east of the depot was removed; "needed the parking space". Then they moved the spur in Osier in order to locate the potty car closer to where the train stopped. It goes on and on with one innocent change after another, until somebody wakes up and says "everything's changed!".
I believe the New Mexico SHPO first got involved when the Friends started restoration projects at Sublette and Cumbres. Initially they were a pain in the butt because they demanded plans and had existing policies that new construction be made not to fool the uninformed that something was not original.
A lot of the justification for this change was felt necessary to support the tourists that bring their dollars to this area. Folks that can remember things from the beginning of time (1970) see much more than folks like me that are rather recent (1985). When you've got a new commission and operations people every couple of years, they won't understand what's already changed. And so more innocent-sounding changes are proposed. Fortunately there are now some checks in the process, but maybe not enough.
But I feel the most severe threats are out of the control of the commission, operator, and Friends, e.g. Los Pinos.