I never saw it as a problem for nginx to just serve web content and let certbot handle cert renewals. Whatever happened to doing one thing well and making it composable? Fat tools that try to do everything inevitably suck at some important part.
Having distinct tools for serving content and handling certs is not a problem, and nothing changes on this side. Moreover, the module won't cover every need.
BTW, cerbot is rather a "fat tool" compared to other acme tools like lego. I've had bad experiences with certbot in the past because it tried to do too much automatically and it's hard to diagnose – though I think certbot has been rewritten since then, since it has no more dependency on python zope.
I switched to Lego because it has out of the box support for my domain registrar so I could use DNS instead of HTTP challenge. It’s also a single go binary which is much simpler to install than certbot.