Obstinate pests unite!
1) I will address your first two quotes-replies at the same time because they're about the same issue. When I say universe, I am talking about a continuity, which I am using here as a synonym to timeline. Take the two as yet aired Spiderman series. They're not part of the same universe where my rules are concerned. They may be two separate franchises - whether or not they are is besides the point I am making - but what happens in one does not impact the other. How can they both belong to the same universe when they offer contradictory versions of the same characters, arcs, etc.?
Retconning is a different issue. Retconning is a way of maintaining continuity whilst altering some element for whatever reason. Much as I hate it when it happens, it does not a franchise unmake, at least semantically. Qualitatively is another matter.
When a franchises contradicts continuity, not in a retconning way but rather in an overlooking what happened before way, that's just sloppy writing and poor supervision. I am still mad about AoU not recognising the changes extremis allowed Start in IM 3, such as getting rid of the arc reactor. Although, considering how well the entire movie ties in with the franchise, it is probably Shane Black's fault more than anyone's.
2) The expanded universes issue. This happens not only with Star Wars but with some other universes too, the MCU included. There are two types of it. There are expanded universes that are officially connected to the movies - take the Star Wars comic books released just before Star Wars VII to fill in some blanks. Then there are the EU where some creative types took the universe and went with it but in a less official capacity, ie, the rest of the SW EU. There have been lots of SW fiction contradicting each other in the past because there was no cannon because most of it was not movie-level legitimate.
I have trouble including non-movie stuff in the franchises, but if I am going to, I want a statement from the creators clearly saying that all the pieces tie into each other.
3) Fantastic Beasts is very much part of the Potterverse as of last year, I am unsure what part of what I wrote suggested otherwise to you. Some of the magic is gone, but the movies are 100% in the universe. And I don't know what that movie you mentioned is.