This. Almost everyone needs WAY more arch support for riding than they think. You should not use the cleat rotation to force your foot away from its natural angle--that's a recipe for injury. The way to approach it is to provide sufficient arch support, then canting if necessary.
As others have said--cleats should be positioned such that your foot's natural position is in the middle of the available float. I suspect you'll find your heels moving away from the chainstays and lining up straight after you deal with your arch support and canting needs.
As others have mentioned, you may need to add some of the features that the s-works shoe already has.
1.) Arch support. Arch support is so good on the S-works shoes that many riders end up not using their custom insoles.
I suggest some sort of supportive insole for you.
2.) Varus wedge. Specialized has varus wedge built-in. Might need to put a wedge under each cleat.
3.) Cleat position. Every shoe is different. Often times even lef and right shoe from same pair. You can't use visual inspection or matching up what looks to be the same. Need to setup in the spot that puts ball of foot relative to pedal spindle that is best for you.
4.) Width. The shoes may have an effective stance width difference due to design of the shoe or placement of hte cleat holes. Sounds like you need to be wider. Move cleats more towards inside of shoe (to move foot more outboard). If you need more than this add pedal spacers. Need more than this- investigate a pedal with a wider axle.