Swiss Germans tend to get along less well with other Germans because ALL different types of Germans tend not to get along super well.
To understand this question, you need to stop thinking of Germany as a country, and start thinking about the Germans as a large cluster of ethnic/tribal/linguistic groups.
The Swiss are one small group, and Germany encompasses the bulk of the rest in a large political federation, though Luxembourg is another separate one, as is Alsace and Austria and South Tyrol.
We all have our stereotypes about each other, born from (very) old conflicts and perpetuated ever since.
Every time there is an interaction, or somebody moves to a new place, those come out.
The Swiss/German issue is the same as every other intra-German conflict.
Any time one German visits the lands of a different cultural group, where a different dialect is spoken, there is the question: Which language do we speak here?
It instantly implies a lot about the balance of power. It used to be that Germans would speak their own dialects to each other and just try to figure it out with hands and feet.
The solution was a public school system forcing everyone to learn what is called Standard German, or High German, because it was synthesized based on the dialects in the middle highlands (Central Germany today).
This is supposed to be a compromise that lets everyone switch to a neutral option, but native speakers of dialects don’t see it that way.
Us “provincials” in Germany, are ok when people speak it to us, as long as they don’t complain about our accent when we reply (Which they do).
The Swiss in particular, see High German as associated with the German Federation, so to them, whenever Germans show up speaking it, it seems to them like a stranger walked into their house and is demanding that they speak a foreign dialect.
German speakers of dialects (especially the Swabians and Bavarians who make up the bulk of visitors), do NOT see High German that way. They see it as a compromise to use it within Germany, and just as much in Switzerland.
They are using the neutral language that is meant to allow speakers of different types of German to communicate. A convention that FAR predates the existence of Germany.
This means that Germans who visit Switzerland see themselves as politely following established convention, and the Swiss they speak to see it as the opposite of that. Mostly because they seem to have forgotten that Standard German isn’t our native language any more than it is theirs.
Hence, conflict.
I think the Swiss are afraid that the Standard German will assimilate their country and culture like it has many of the groups within Germany, especially in the North where some dialects are approaching complete extinction as they are assimilated by the bland academic Standard. The same fear is common in Germany.