If you don't mind the extra 8-9" width of the Flatbed (also a bit larger broken down for transport) then, yes, go for it. There are a lot of vendors of dry bags, including Ortlieb, REI, Cabelas, backpacking and rafting shops, etc, so you should research these a bit before giving all your money to Burley.

I long ago had the same thoughts as you on Nomad vs Flatbed WRT size, weight and volume capacity, cost etc. Nomad is not waterproof and if you're going to bag everything anyway then the Flatbed looks like a good alternative. Also Flatbed would make a pretty handy grocery/utility hauler.