Ya, the 690 is an SLI board on any MB it is on, not really theoretically but physically, your system sees 2 cores out there in SLI just like it would see 2 separate cards in SLI. With 2 cards you could run them separately if you wanted, I don't think you can with a 690, it is SLI only.
Another thing to consider, heat, you have 2 hot cores on 1 board and only so much cooler, on 2 boards you basically have twice the cooling capability because you have 2 coolers. Just take an objective look at this in reference to your 690, as you must know the 295x2 from AMD is factory WCed, that is one reason it even works, but as on par with AMD it is half assed. Visiontek did it right with a full cover block to let the 295 fly, what a difference a bit of cooling makes.
http://www.tomshardware.com/reviews/visiontek-cryovenom-r9-295x2,3951.html
Same thing with a 690 or any duel core board, you have twice the heat to deal with and only so much cooling.
My opinion here about any duel core board, they are the fasted single card solution you can get, IF you need it. If I have only 1 PCIe x 16 slot and want SLI then the Titan-Z or 295x2 are my only 2 options. I can't think of any other reason off hand that would benefit me getting a 690. Also, I would not buy a 680 today much less 2 of them in a 690 unless I had to simply because of performance (the GK104 is a bit dated today) and heat (300W TDP) on 1 board. Also only 2GB per core, it may be fine today but memory needs are expanding with the higher higher density screens, 3GB per core would be better.