Options[plot, ImageSize] only gives the option, which was chosen in the command and does not help determining the ImageSize in the y-direction.

I still have the problem with the added vertical space using your options. Its best visible after exporting as a .png and comparing the size. Maybe you know a command to combine 3D and 2D graphics, while still maintaining the vecor graphics. Show and Graphics cannot combine 3D and 2D plots. Using Inset in the 3D plot destroys the vector graphic properties of the 2D graphics.

I use Overlay to combine a 3D Graphic (e.g. ListPointPlot3D) with a 2D Graphic (e.g. ListPlot). This way I can have 3D graphics, while keeping the vectorgraphics properties of the 2D graphics in a pdf-export. Therefore I wanted to understand, why Overlay already has a vertical offset when using only a simple 2D graphic.

Changing the PlotRange to {{-50, 50}, {-300, 40}} instead of {{-50, 50}, {-265, 5}} fixes the problem, without being able to explain why.

Any ideas for a workaround? A circle does not have this issue.

If I open the exported pdf with a vector graphics program, the issue is the same. But thank you for the effort!

I use Mathematica 12.1 on Windows 10