Does a red shirt Junior (Academic Sr/Athletic Jr) have more bargaining power in the draft than a Senior?
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Probably.
He has the leverage of returning to college. But the next year he will be a twenty-three year old in short season A ball. If he doesn't blow through three levels of A ball quickly he's looking at a release. Being a senior provides no leverage. Being a 23yo senior is even worse.
The draft is set up in such a way that only a very few players have what one could fairly call "bargaining power," but generally yes.
To illustrate, in the tenth round of this year's draft, the median bonus of college juniors (including redshirt juniors) was $125,000. The median bonus for college seniors in the same round was $10,000.
However, there are lots of other baseball and business variables at play that can affect the bonus greatly, as shown by the circumstance that one junior got only $25K while a senior drafted later in the same round got $138K.
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