Just to be sure: You have a custom texture button scene looking like this
and instance it in a different scene as child of a VBoxContainer like here
The size of elements is too big, despite me setting the scale
Then I assume by "elements" you mean your CustomTextureButton's inside the VBoxContainer? If so, setting the scale won't do anything. Again: any container can overrule any modification you did to the transformation of it's content.
by "not set properly" I meant that it's not set at all.
I cannot reproduce that. I created the scenes as described above and added the script you provided to the CustomTextureButton, prefixed with the
tool-keyword. It works fine, both in the editor as well as in-game. Can you provide an example project?