I'd recommend sending an email to Waterfield design. Ideally, include the dimensions of your iPad in the Vaja case. I'm sure they'll respond promptly. Their customer service is excellent.
P.S. My guess is that you should go with the 11". In my experience, their bags are very form fitting.
The Muzettos are generously sized and not form fitting like their sleeves. Most standard folio cases will work fine. The only case I can think of having problems fitting would be twelvesouth's bookbook, and the bookbook is only slightly on the tall size for the portable.
I have the 10' muzetto and you should be fine with the vaja i fit both my ipad with a case and my 13' macbook air and still have room for the keyboard in the waterfield keyboard sleeve. the macbook sticks up alittle at the top but the flap covers it still