Hi guys. I've just ended to read everything of this topic. I'm new in the world of PkHeX and I was scared about using it.
I've downloaded it just yesterday, before this post creation. I've created a few LEGIT pokèmon such as Arcanine and something else in order to be legit.
I'm playing on Pokemon Sun and what I did with Hex was just create some legit pokemon with some item with them like assault vest etc.
I didnt get banned even If I used the global link. I've alsod did a trade with a friend. So what I think is that ppl who got banned just did a wrong usage of sav like hacked pokedex and some locked pokemon such as Shiny tapu. I dont know if this might help you a bit.
With Hex I haven't changed my char name/location and other stuff.