Keep app "always on top" in El Capitan
You could try to achieve this functionality with an application like "Afloat" as you mentioned already. But it seems to only work in El Capitan if you permanently turn off System Integrity Protection (SIP) which isn't recommended.   

However, here is the link to the program: https://github.com/millenomi/afloat

How to turn off SIP: https://github.com/millenomi/afloat/issues/22