So you already have both? Just link em', whats the problem? I'm more annoyed that they got rid of finding your Twitter followers on Instagram.
Just because you have both doesn't mean you want to link them.
It makes perfect sense to keep it separate. He probably doesn't want his Facebook friends to know about his Instagram usage.
Facebook recently announced a new Ad model to investors where they extract all data possible from 3rd party apps, and apps that require a Facebook login/connection. To give the user more targeted ads. Who wants to see more ads?
I've become absolutely frustrated with several websites and apps saying "login with Facebook".
Anyway, I don't use Instagram so I can't comment on how to bypass that. I guess you have to make a fake FB account if you don't want to connect your real one.