Grid padding is simply applied to the container as padding (padding: $grid-padding;) so you could remove that and apply it to the margin instead. I may consider adding that as a setting...
Best practice is to use semantic classes in your markup, and then apply the mixins in css. You can use placeholder classes to extend, but you'll need to include context in your classes as well (%span3of6 etc).
That leads into your last question. You need the context when nested, so "
+span-columns(2, 6)".
Cheers,
-e