For anyone running into this - this bug is still there for me in inkscape 0.91 in March 2017. Only, that I don't even need to save in between, the image bounces back immediately to it's original aspect ratio as soon as I release the mouse. The workaround still works - go to Edit-->XML Editor, then a...

I'm having the same problem: I'm working on an image with transparent background. Eventually I want to use this image in another application on a dark background (think: white text). So I want to set the background transparent and the canvas dark. As far as I can see the background of the workspace ...