From what I understand it's something Google is working on. I've been dealing with the limitations myself for a while and it sucks, but hopefully it'll be fixed on their end sooner rather than later.

Specifically I'm looking at GCloud SQL, which does not yet allow you to use config options that require system-level changes. You can still use a dedicated SQL GCE instance, but using the managed SQL itself isn't yet possible without running into errors about the sql_mode.