In this case, I was just interested in overriding some of the basic CSS classes that are across the entire theme (website would be more exact), mostly Bootstrap components like the “row” or “btn” with minor modifications.
Correct me if I’m wrong, but I try avoiding changing specific elements in the original CSS files (e.g. templatesja_cagoxcssbootstrap.css or the CSS inside a module) because I don’t want to mess something up keep track of too many changes across the files in case of revisions. I just try to “play it safe” on the expense of creating some extra overrides, and counting on the order in which custom.css is loaded.