I dug around a little bit, trying to understand how Mermaid rendering works, it is quite messy. Thank you @dpoulton for the information on manipulating the rendering of Mermaid charts through userstyles.css
The issue is related to fractional scaling in Ubuntu. I am using 125% percent scaling which causes the mermaid rendering issues. If I go back to 100% the rendering is just fine. If I use 150% or 175% scaling the issue exists, too.
This seems to be a problem with electron and the chromium team is working on it.
As I stated above, mermaid rendering is quite messy and I dont fully understand it. But I would expect that fractional scaling influences the width and the height of mermaid nodes, which is not the case.