As this is the Ultimate Edition of the game we have access to the 2 expansions: AWE and Foundation. Ability points earned in these expansions will help towards the 100 total.
Worth noting that resetting your points and spending them again DO NOT count towards the 100 total.
You can earn ability points by finding hidden areas, completing main and side missions.Here are some video guides for hidden rooms found within Control (Not by me):
Main game:
AWE DLC (Investigations):
This will also unlock:
Foundation DLC (Foundation):
This will also unlock: