I am trying to enable some features for Subscriber user role in a eCommerce theme where originally had be set for Admin role and I like to modify that. I tried AAM plugin but for this specific site it does not show those features so I can place a check or un-check them. I know AAM or any alike plugin serve as an interface and there are ways to look through the files/codes to make this happen. I found in wp-includes/capabilities.php is where this gets managed but I am assuming not for each specif site as I can't find anything about other sites in there. Does each site have its own capabilities.php somewhere?
I believe you'd need to modify user roles on each site individually (if I'm understanding your question correctly).
There's a great plugin I use frequently called WPFront User Role Editor that allows you to check/uncheck user capabilities like you mentioned. The free version should be fine for what you're trying to do. I personally use the paid version just because I like to have the extra options when I need them, but 90% of the time the free one works fine.
AAM is by far more powerful and it's since version 6.3.0 fully compatible with WordPress multisite as mentioned on its website.
It also has the functionality to sync capabilities/permissions across all sites on the network as described on the above mentioned article.