Well, aside from yEd, Inkscape, and Firefox, I also tested with Chrome and Emacs. Chrome sides with yEd and Firefox, while Emacs displays the document like Inkscape. Unfortunately, I know way to little SVG to decide which viewer is right. (Actually, I think even an SVG expert would be hard pressed to decide which visualization is correct due to the many transformations used inside your original SVG documents.)
My only idea to improve the situation is resizing your four original SVG documents in Inkscape in such a way, that they are equally sized (and placed) in Inkscape and then used those modified versions in yEd.