craftgrrl | Embroidery trouble shooting

My boyfriend is badly in need of some sort of messenger bag to carry files back and forth from work with. I'm wanting to get a plain one and embellish it with something 8-bit and nerdy (he is a big fan of old school video games.) The problem is that every bag I'm finding has external pockets on the flap that will make it impossible to embroider. Anyone know tricks to embroider over a pocket without making the pocket useless? Know of a supplier of basic messenger bags without flap pockets? Should I give up and make a stencil instead?

I had my heart pretty set on emulating the blockiness of the art with cross stitch. I've even been working on developing my own stitch chart.