I get a lot of questions from folks with quick release bikes from Specialized, like the 2015 Diverge, or Cruz, or Roubaix, or the 2016 Crux Alloy frames, etc. Very simply, yes, these bikes SHIP with SCS wheels (usually the Axis 2.0 alloy wheels), but they are NOT SCS FRAMES!
Basically, as Specialized product manager Mark Cote says, they decided to apply the SCS road solution (which I believe is the best solution) to the cross and gravel bikes to help push it forward.
“At the end of the day, we created a standard that we thought was the right thing for road bikes and decided to use it for our ‘cross bikes, too,” says Cote. “As the entire industry is working towards a standard, we knew we’d learn a lot eventually leading to a committed standard for disc brakes in the industry. All riders committing to new thru axle cross bikes are experiencing compatibility challenges with their older wheels going into this season. This isn’t unique to the 2016 CruX – But you know what? (The Crux) rides amazing, there’s no brake or heel rub issues and the people racing it are really enjoying it."
The rear end of a quick release bike is simply 135 OLD (over locknut distance) whether it has SCS wheels in it or not. That is to say, it is just like and disc equipped quick release axled mountain bike (do they even make those anymore?). So how do the SCS hubs, which are, end of the day, a 130mm OLD road standard hub with a disc brake on it, fit into a 135mm OLD frame and still shift correctly? Simple - Specialized made a special derailleur hanger to convert the FRAME to the WHEELS (as opposed to special wheels to fit the frame). I get why they did it, and Cote explains it in his statement above. The derailleur hanger kicks over a couple mm to move the derailleur over (inwards) to where a 130mm road frame would place it, relative to the cassette on a 130mm road hub. That is all. That is the only thing making your QR bike an "SCS Frame".
The moral of the story is, if you take off the SCS hanger off and replace it with a good aftermarket or Specialized "non SCS" hanger like ones from Wheels Manufacturing (#146 for an alloy Crux) then you have a 135 OLD quick release disc brake bike, the same as all the other brands out there using that very common standard.
Once you do that hanger swap, your Axis wheels will not work unless you reset your derailleur limits over, but then the bike won't work with other wheels unless you again reset all your stops. So the way I see it, given the shifting adjustments required, you have two logical options. Option 1: ride your bike the way it is, on the Axis wheels with the SCS hanger. Option 2: swap to non SCS hanger, upgrade your stock alloy wheels (the Axis 2.0 are something like 2100 grams) to a nice aftermarket wheel (ideally our 38G at 1,650gr on DT 350 or 1,575 on DT 240s), and save the Axis for resale down the road.
Hope this helps clarify SCS on quick release frames!