I don't think you will notice a difference ride quality wise between the two bikes, but handling wise there will be a difference. I really think only you can decide what type of bike you want. The big difference between the bikes is the head tubes, the Roubaix is longer. You may require that longer head tube and getting the Tarmac to fit is possible, but may not be optimal.
I myself have my two bikes the (Roubaix/Tarmac) setup pretty close. The Roubaix stem is flipped down and the Tarmac flipped up. I could not achieve this last year (2007 model) since the Tarmac head tubes have been lengthened for 2008. For me the Tarmac is not the optimum bike, but I'm playing and seeing how things go.
The LBS must really want to unload that Tarmac if they have it priced the same as a Roubaix Comp. Normally there would be roughly a $600 difference between the two (looking at 08 MSRP)