Greg, I would not cut the base away on the RS3 plastic stanchions. Instead, file off the U25B catwalk detail flush, and then enlarge the hole, if need be, to accept the square / rectangular peg at the bottom of the stanchion.
But thinking a bit more of what Rooster suggested, I suppose holes could be drilled in the sides of the U25B sill to accept the USA Trains side / end rail stanchion right angle prongs. That way they don’t need to be bent straight. Doing this, I suppose spacing between the stanchions could be left as is with the USAT railings, too - ignoring the U25B spacing. The problem may be figuring out how to deal with stepping up over the boxes near the rear of the loco.
As to bending the USAT railing wire, if done carefully with 45 degree angle, it should work to transition over the boxes. Using longer “donor” SD70 or SD40-2 railings would seem to allow for enough excess to optimize position of the stanchions in optimal places to be more pleasing to the eye.
Just a thought,
-Ted