I think MLB can avoid the issues that maybe contributed to the decline of baseball in Puerto Rico. There are a few reasons.
By being included in the MLB draft, Puerto Ricans had to wait until the typical draft year (conclusion of high school), so they competed with all the North American players. This wasn't really fair to the kids since high school baseball is almost non-existent there. Teams also no longer had any incentive to invest in academies for cultivating talent in PR, since any other team could just draft the players. Teams also had other countries that they could simply move to - DR, Venezuela, etc., and they did so.
If the international draft is separate from the rule 4 draft and lets players be selected at 16, then I don't think there would be any negative impact. What would make it even less likely to have negative impact would be to simply have a money slot system where players can still pick which team they want to sign with - this would keep incentives for MLB teams to cultivate talent with academies, etc. I'm suggesting that teams be granted slots with specific dollar values like in the MLB draft, but these are treated like limitations on allowable agreements, so there is no draft per se. If the team has slot 1 with a value of $8M, then they are permitted to sign any one player for up to $8M.
Heck, PR could even be thrown back into the international draft.
There's also the chance that PR's baseball decline had nothing to do with the MLB draft, which you allude to.