First, every team breaks the rules as far as international signings go. Pretty much every one of them signed has a deal in place with a team prior to signing day, often for years. MLB is aware of this and lets it happen because teams need to be able to allocate their money and plan ahead.
Bundling is where you get in trouble. It's what we did this year but it's not what we did in 2016. We had no need. So declaring guys from that class free agents would be based on other violations. Violations that generally don't draw a penalty of declaring the prospect a free agent.
Additionally, MLB doesn't look great no matter what. They've created a terrible system that encourages rule breaking. We should already have an international draft.