I have used an Altura Urban 17" for the past year, carrying my laptop. It has been entirely waterproof. It mounts on the rack at an angle to allow more heel clearance. For the money I think it is a good option and totally reliable. No sign of any wear as yet (been used 4 days per week on 14 or 20 mile commutes in all weathers).
There is a flap that zips over the fittings on the back (but I don't usually bother). You can feel the fittings but I can't say that it has ever proven to be a problem, comfort-wise. Of course I am just carrying to and from the bike and around my work place (or the Supermarket) so no long walks, which might then pose an issue.
I use the Vaude Freiburg which cost about £45 two or three months ago. It looks neat, is big enough to carry a couple of files for work and stays on the bike unlike the normal laptop case and bungee arrangement I was using before. However there is already evidence of some straining round the handle so I couldn't really recommend it.