Good morning Tiapriestess!
I thought I’d take a stab at your questions too as I think the GM might have been wrong about it not being automatic. The way I see it is that the complete edition adds BFA, Epic Shadowlands (is the one you mentioned getting), game time and 2 boosts (110Bfa & 120SL).
I honestly believe that the system would only care about which version of SL you have. So when you add the CE key, you would get the refund based on having Epic Shadowlands.
“If you purchase any digital copy of Shadowlands (Base, Heroic, or Epic), and then upgrade to the Collector’s Edition in the future, we will automatically credit you the cost of the digital copy in Blizzard Balance” Source .
It really shouldn’t matter that it was purchased as a bundle. I know the GM says otherwise and I’ll admit I could be wrong, but I don’t see why it would matter to the system.
If I’m wrong, hopefully one of the Blues can shed some additional light!
And if I’m on the wrong page for what you’re asking, then my apologies 
You also mentioned problems when entering the ticket where it removed spaces. I was wondering if you were using the following screen:
If it was, I’m not a huge fan of this box as it should probably not state “detailed”. I find the system gets more confused that way (imho). I tend to just use the “I would rather categorize the issue” link below the continue button. Then I can see the subsections for tickets and choose my own adventure!
If it wasn’t that box, then it’s very odd that it would have kept removing spaces in an actual ticket. Not sure what would cause something like that to happen.
Hopefully this doesn’t sour your experience too much and even more importantly, I hope you’re able to find a way to return and enjoy the game again.