I wouldn't say Stewart is better than Mountcastle. Mountcastle has never played right and they probably don't want to cause him to deal with that sort of distraction.
Is career CS are a bit over league average and a bit under this year. Mountcastle is faster this year but he only has 29 total stolen bases in his pro career, so I don't think he's a threat to run.
I think they can be developed better in the majors than with what they are doing at Bowie. I think you quickly hit a point of diminishing returns with the type of setup they are forced to run.