JCA is right. There's no curve or special consideration for "about to be an MLB regular" or "these players are going to graduate soon." It's a simple, hard cutoff separating rookie eligibility and non-eligibility.
Taking into account how the farm system might look in a year or two after a bunch of guys become MLB regulars is something that's left for a year or two down the road, when it actually happens.
Im expecting that Ciolek and Haas will have transforned the farm system in a couple of years