This issue came out as a part of recently added Stage Attributes test (see related issue).
When a new Stage is created (not the one supplied via Application.start() ), its dimensions are different than declared inside Scene constructor. It also reports width/height via API as intended, however the actual window dimensions are not reflecting that.
Running attached test program shows two Stages - the bottom one is provided via start() argument and it properly accepts the dimensions from the Scene (in test program case, 400x400). Top stage is created right after the bottom one is set up, with the same parameters (400x400 scene). However, its dimensions are half of what they are supposed to be (see attached picture).
Issue happened on Fedora 38 (Linux 6.4) VM with X11 window system. Attached program works properly on Windows.