In the past the rule 5 draft had one less year of protection. 3 for college and 4 for HS/Latin American signings. That year makes a big difference. The prospects that look like front line starters have generally been revealed after 5 years and they get protected. After 4 years they might have been identified, but it was a much tougher roster decision for a team to put them on the 40-man before they are ready.
If we lost that extra year of protection then a whole slew of prospects might go unprotected. On the Phillies I might guess that Moniak would have gone unprotected since we need that 40-man spot to cycle relievers on and off the major league roster. Moniak does not look like more than a 4th OF now, so the risk of leaving him unprotected would be minimal even if he might be able to survive as the 26th man somewhere.
Marchan is promising, but is still not ready and also does not project to be an above average regular at the moment. He is not really a late bloomer. Just a 2nd tier prospect that can't help anyone on the major league roster now and is not good enough to stash.