So did the GM do good?

You mean a FM spot sniper? Nah man. He snatched up the spot. He doesn't get to keep it.

IDK how long vacant spots in Scania FM4 usually stay vacant.
Nothing morally wrong with taking a free spot. Mind you, it wasn't even a spot that was only momentarily free because someone was resetting their shop. The permit shop disappeared when its owner "logged off".
Atquei didn't even tell him, "But you've nothing to sell, you're just holding the spot." He acted as if he'd do the same regardless who took the spot he made vacant.

I guess I can't come to terms that a GM would be logging into my account, that is incredibly odd to me, from my understanding, even on private servers you had the capability to do 'item research' without even logging in. Plus they have access to your character info? Idk the whole scenario is uncomfortable to me

I am uncomfortable with the idea as well. I never said I approve of it, just that it does happen. I think it should come as no surprise that private server GMs have better tools at their disposal than Nexon's GMs, who seem to have little to no access to the database, and must get in-game for just about everything.
I don't know whether they have access to your password or just a way to log in without ever entering it. I would assume the latter.
They don't have access to the PIC, so they have to reset it to get on your character.