I don't want to read through the MLB rules for this so here goes:
What prevents a team from drafting a player, signing them to an ultra low bonus, and then paying them a higher wage in the minors? This subverts the bonus pool system but still compensates the player.Agents might be wary but teams have been pushing the slot bonus rules for their whole existence.
A player would just have to say no. There are rules in place for the minimum amount that must be offered in the first three rounds to recover a draft pick the following year, and it'd be foolish to go below that.
While there is no set minor league pay scale as each team determines that on their own, the reason the Blue Jays were more free is that they are in Canada and MLB pushed for legislation in the US that made it legal to pay far below minimum wage for minor league players. That said, the Jays' bumps are still incredibly low pay, as in a player who shows up in February, spends time at spring training and then extended spring before joining a short-season A-ball league and then follows up by attending fall instructs will spend from early February until mid-September/early-October under the team's control, but for significant amount of time in there they aren't being paid (spring training/extended spring/instructs are all unpaid), and being in a non-full league is very low on the pay scale, so it's entirely feasible that player would spend 8 months of their year working full-time in order to earn $3,000. With the Jays' bump, they're up to $4,500 for that 8 months, which is definitely better, but it's still not even $600 per month.
What I'm saying is that the minuscule impact that $1,000 more in the first two years or even $5-6K more in upper level minors will be is not going to replace a slot signing bonus in the first two days of the draft.