Let’s say I have directus_users, countries collections, every user related to a country.
I want to make a panel to tell top 5 countries my users from, how can I do this?
I tried to replicate this with Choropleth Map Panel Extension but I didn’t succeed, because the extension deals with directus_users as normal table, so it’s calling it using /items/directus_users
Sounds like an interesting use case!
In this case, it’s seems like you’ve answered your own question to a certain degree 
You could probably just fork that Choropleth map panel extension. And update it to support querying the directus_users collection (or any other collections you need).
You can certainly open up an issue in the repo, but we don’t have any timelines of when or if that would be something we could address.
For what it’s worth, forking and customizing extensions is pretty straightforward.