It’s not a problem to set something like:
position:relative;
z-index:20000;
background:red; /* just for the test, of course */
for your main menu items’ links but, as I mentioned, the scrolling feature for the sub menus only works against the viewport so you will have troubles accessing the top items once a sub menu is scrolled up since they would appear beneath your main menu items.
So, unfortunately, this cannot be achieved with the current code. But I’ve now thought about the scrolling feature a bit more and it might actually be possible to achieve what you would like for horizontal main menus – i.e. we could use an additional clipping container (appended in the main menu items’ LI and wrapping its child UL) displayed right below the main menu, taking the full width of the viewport and the remaining height below the main menu and then we could display and scroll if needed all the sub menus inside it. On theory this should work as I am thinking although it will probably be a bit tricky to implement and might break some user CSS since we would dynamically add another wrapper DIV that users wouldn’t be aware of. But anyway, this is something I could try to implement in a future release.