Theres no easy way to transition between the logo being within the Mobile Header and not. You could change your CSs to this:
.navigation-branding img,
.site-logo.mobile-header-logo.is_stuck img {
position: absolute;
height: 125px;
top: 0;
padding: 0;
}
The change being .site-logo.mobile-header-logo img becomes: .site-logo.mobile-header-logo.is_stuck img. This way it only absolutely positions the logo when the Mobile header is stuck ( albeit it off the screen on scroll down ).