No more holes, just that both my comments were related to real life (non experimental) observations:Anymore holes you can pick?
I know that when I cook if I put the lid fully on the saucepan it will not (usually) boil dry, however if I don't put the lid on (and still cook/boil for the same time/intensity) then most often things will boil dry on me (I even managed to boil dry some soup the other day - go figure!). So from that perspective, I'd have thought that having the lid 'fully on' would make a huge difference to any losses, not just minor, minimal or perhaps no change as your experiment showed.
When I 'boil' my wort, with my kettle/setup/ideal boil, I do not see masses of bubbles on the surface as per your beaker experiment, what I see instead is a large 'convection bump' from the hot wort rising from above the (electric) heating element and breaking the surface - kindof like one big continuous bubble. So I was interested/concerned as to how putting a lid partly on would impact the convection currents within the wort, since in my case that is where most of the mixing comes from not from the 'bubbles'. But as you pointed out for your experiment most of the 'mixing' of the water is due to the bubbles rising from the bottom rather than any 'convection currents'.