It overwrites the quest that handles training progression, both for SPECIAL stats and now for solider ranking. The mod worked fine before Chapter 3 but overwrites the changes made for Chapter 3 with its modified version of the Chapter 2 quest.
Best practice is to use the SPECIAL zapper or console commands, and keep "house rules" for balance — e.g., I donate 500 caps to my settlements for each level of special up to level 5; 1000 caps for each level from 5-10; and no increases above level 10. Really makes you "invest" in your people, and the cost is high enough where you have to think about taking a settler to 10 and how much value you'll get out of their training.
Edit: I wonder if an "advanced training" plot is possible without touching the quest… then you could have a plot with ridiculous upkeep costs to get your settlers trained-up.