In your demo with nano3 on
your logo appears centered on the right side of mobile-menu (position "offcanvas") and it looks very clean and nice.
If I try to replicate it, I am placing the mobile-menu in position "offcanvas" => this works for me
when I use the position "logo-small" (as recommended in Yootheme Forum) for displaying a smaller logo for mobile devices it looks like a second layer in position breadcrumbs.
I have attached a pic showing the difference between my and your vmuikit-logo position on a Samsung Galaxy.
I would really appreciate to learn your trick about the proper positioning of smaller logo for mobile devices.