Adding a custom location rule seems to have changed quite a bit since I’ve set up custom location rules… luckily my legacy code seems to still be working on sites where it’s used.
But because of the way that ACF works is seems like if it’s using the location rules that it should be checking all location rules, including custom rules. I say this because ACF’s rules are run on the same hooks as those that would run custom rules. The only reason I can see it wouldn’t is if there’s some reason the your rules have not been loaded prior to calling acf_get_field_groups().
This could possibly happen if you try to get field groups before acf/init is run which will force a premature initialization of ACF that can have unexpected results.
