CodenSnap, (I now this is an old thread but in case this might help others)
I'm working on a similar setup (domain registered with Google and hosting DNS with either CloudFlare or AWS Route53). In domain.google.com there is an option to switch your DNS to "manual". Once switched to manual you have the option to entered to DNS servers for for your domain. I can enter either Route53 or ClouldFlare. In either service I then add my DNS instance and create my Zone. From there I was able to use Dynamic DNS, add A, AAAA, & TXT, records ,etc, with either DNS provider. Have not yet got the ACME client to work. But best-I-can-tell there is no negative with registering a domain with Google and then hosting your DNS with another provider.
Best Regards,
RKGraves