When you’re crashing out and don’t know why, run in debugger, and cause it to happen. That will either give you a lot more information, or send you on a wild goose hunt 
However, this also points to the problem:
Having this happen, it’s definitely related to using a custom game instance class + PIE. I’m not even overriding anything.
Well, that’s what the error means – it’s expecting you to override functions.
virtual void Init() override;
virtual void Shutdown() override;
virtual void StartGameInstance() override;
Those are virtual override, so if they are called, an implementation must be found, or you will have a crash.
Understanding the error messages is key to locating the problems But also so is using your debugger.