I won't argue too much about the Sumpter Valley roster because there are obvious errors in most of the information that has been printed over the years. Besides, you're one of our experts.
As I sorta understand it, the original roster was primarily former Utah and Northern engines, then 1-4 were renumbered to allow the Tonopah engines to keep their original numbers plus they picked up a few more odd used ones and sporadic renumberings. Then they traded some of their smaller engines for larger ones from Eureka-Nevada. So the question is, why did they bother trading for the C&C/E&P/E-N 4-4-0 if SVRy didn't have an appropriate use in mind for it? The first new engines Baldwin Mikes 16-18 make sense as to their numbers, but then they jumped to 50. The Alcos came as 100-101 so they might have been already numbered that from somebody elses cancelled order (pure speculation by me) or were part of a bigger plan intending to renumber all the other SVRy engines other than the 50. This might have so that the lower numbered engines didn't get confused in train orders as Extra 3 is very different than train No 3 and confusing the two leads to at least a near miss if not an outright wreck. But after the fire, 100-101 end up back in the regular sequence renumbered 19-20 leaving 50 still the odd one out. The Whitcomb and its replacement Whitcomb end up as second 100-101 but being infernal combustion that makes some sense. Then Mallets 50-51 are assigned 250-251 - what was wrong with 150-151? Too bad the SVRy didn't survive into the diesel era as I'm sure they would have confused things even more - maybe starting back at #1 or 720?
And some of the logging lines history was far worse. I wouldn't be surprised if somewhere in the woods there are three different "Old Brighams" still hidden away all with the same numbers and builder's plates - unless of course Martin has all six plates in his collection