Hi,
My biggest problem with the current design was that it took too much horizontal space. When using Inkscape on Ubuntu, at least, you get mad spacing and padding everywhere and there's scant little space left for the actual canvas. In that respect, your new desing show little improvement. I'd favor any design that made this dialog less wide.
I agree with this, the canvas should have the most screen space, not the chrome.
There's a lot of useless padding in your design,
..I wouldn't agree with this, all the padding is in there for a reason, so elements can easily be distinguished etc.
and the bottleneck seems to be the self-intersect button. Move this away from the fill type button row and you could make the dialog narrower. Perhaps it could be moved between the out of gamut warning label and the hex code? Not an ideal place, logically, but it would help with the width issue.
I should point out that these are only mockups, so the dialog may become narrower when it is actually implemented.
Regarding your suggestion, I don't think this would make any difference. It would just mean the width of the dialog would shrink to the width of the bottom row (with the new intersect buttons in). However that row would now be quite wide, so as well as not really shrinking, the buttons are now in an illogical place.