For simplicity and cost, we are starting our project using local MySQL running on our GCE instances. We will want to switch to CloudSQL some months down the road.
Any advice on avoiding MySQL version conflicts/challenges would be much appreciated!
The majority of the documentation is for MySQL 5.7 so as an advice I recommend you use this version and review migrating to cloudsql concept this is a guide that will guide you through how to migrate safely which migration methods exist and how to prepare you MySQL database.
Another advice which I can give you is make the tutorial migrating mysql to cloud using automated workflow tutorial this guide also says that the any MySQL database running version 5.6 or 5.7 allows you to take advantage of the Cloud SQL automated migration workflow this tutorial is important to know how works and how deploy a source MySQL database on Compute Engine. The sql page will give you more tutorials if you want to learn more.
Finally I suggest to you check de sql pricing to be aware about the billing and also I suggest to you create a workspace with this you can have more transparency and more control over your billing charges by identifying and tuning up the services that are producing more log entries.
I hope all the information that I'm giving you are helpful.