Keep in mind that MOST of the kids drafted will never qualify for MLBPA membership. The MLBPA does not represent these kids' interests. "The union" isn't representing these kids. That's why "the union" has never treated the draft as a major issue - except when draft compensation has impacted the earning power of their members (who, again, are NOT the kids being drafted).
The reality is the the MLBPA would happily agree to restrictions on bonuses - because restricting bonuses doesn't impact their membership...except maybe to make a few more dollars available to their members through arbitration/free agency. Yes, you could make some argument about the union "thinking about their future members," yadda yadda yadda - but do you really think that the MLBPA's player reps are somehow more farsighted and self-sacrificing than other typical Americans... especially American athletes, who typically have been coddled all their lives and tend to be more self-centered than average, if anything?
When the MLBPA extends membership to all players who sign uniform player contracts at any level, and fights (seriously) for civilized salaries in the minors, then maybe we can talk about the MLBPA negotiating terms of the draft. But as it stands... this is fox in the hen house stuff.