From related questions (see below), I have understood that the meaning of "welcome to" and "welcome in" is dependent on the context. Because of that, the question
What is the difference between "welcome to" and "welcome in"?
is not a well defined question in the first place.
That means it can not be directly answered.
So I will give a precise context, to create a strictly defined question.
This is about comparing the two phrases
Welcome to Berlin!
Welcome in Berlin!
as opposed to the general comparison without specific city.
The Situation is a short verbal interaction with a traveler inside the city referred to in the sentences. The interaction is finished with the discussed example sentence.
It is meant to mean: "You are welcome in this city, I hope you will enjoy being here!" without implication about visiting or staying for long time.
What's the difference between "Welcome to Berlin!" and "Welcome in Berlin!"?
There is a more general similar, closed question: Difference between "welcome to", "welcome on" and "welcome at" It has an answer, but it's not really helpful.
Also similar, but more general and without answer is "Welcome to" or "Welcome in"?