I'm not sure if this is a bug or feature, but the include/exclude were used in conjunction with PRECAMPAIGN without any success.
The docs show this as supported, so I think this must be a bug. I'll have a look into it.
From the docs
I've tested this out using the "Minotaur - Monster Focus: Skeletons" source. /data/pathfinder/minotaur_games/monster_focus_skeletons/monster_focus_skeletons.pcc includes the following entry:
When loading this source plus the core rules only, the bone eqmod is available but not others within the source such as bronze.