I confirm that this solves the problem for me with Adwaita and Greybird. I think this is the best we can do, so I'm closing as won't fix, since it's only an external fix. Thank you Theo.
The fix could be integrated into the source code though. Mousepad already applies styling changes to certain widgets via gtk_css_provider_load_from_data.
I'm not sure I want to hard code this. As I push my tests a little further, I realize that the bug is actually not limited to the maximized case. You have to look for it, but the problem is also present in normal mode, it's due to the centering of the scrollbar in the gutter.
However, by applying this fix also in this case (i.e. by removing the maximized class above), I realized better that it off-centers the scrollbar in the gutter. Perhaps this is a visual effect that some users would not want to have, even only in maximized mode.
After all, is it that annoying to have to select the scrollbar, not the gutter, to scroll the view? I must say that I have never been bothered by this problem, even though I admit that I don't use Mousepad in maximized mode very often.
Anyway, I would be more in favor of keeping this as an optional fix, to be applied by the user as a customization if he really wants it. I plan to mention it in the docs when Mousepad 0.5.9 is released, though.