Which rack top bag fits an 11" MacBook Air with space for a little padding?
Topeak has a laptop bag called an MTX Office Bag that attaches to the MTX racks and lays flat.



It is said to accept a 17" laptop so yours should fit in great and given how thin they are, you should have room for a change of clothes.  You might be able to use a padded sleeve.

I tried to put my older 15.6" Dell 131L in my Topeak DXP pannier and it fit, but not much room for other things.  However, I recommend getting a padded sleeve, and with mine it would stick out an inch or two and really no room for anything else.

These bags are pretty good about keeping stuff dry on short commutes (30 min) unless it rains really heavy (and then it was the bottoms of the pannier due to tire spray), but a large locking freezer bag will do the trick nicely.