To be honest, Bill,
Both techniques are legitimate, both prototype.
If it were me (take THAT for what it's worth). I would do what makes the most sense economically. If you have a deep pool of funds, which Stuhr seems to have, then you can Jack up the car number and build a new car.
On the other hand, if you are leading a hand-to-mouth existence like the C&TS seems to be leading, then splicing sills in the manner of the D&RGW will enable you to stretch your limited funds even further. Just remember to document your work somewhere so if the time comes that the railroad over Cumbres does become more solvent, your restoration and repair work can be considered for a major rebuilding, if required, as time and dollars dictate.
It's just good business to do what needs to be done in the best and most economical way possible. Heck, look what the RGS did with almost nothing for so many years. Even THAT is prototype.
Rick