Hey,
According to the Floyd Rose depths diagram, the studs should be on a ledge at one thickness (0.2650") then the rest of the FR route drops down deeper (to 0.44") to allow for pulling up on the trem arm,
Depths,
http://www.floydrose.com/pdf/Floyd%20Rose%20Original_(route%20pattern,%20depths).pdf
Top view,
http://www.floydrose.com/pdf/Floyd%20Rose%20Original_(route%20pattern,%20top%20view).pdf
You can kinda see the ledge the studs are on in this pic,
Do you follow the Floyd Rose dimensions exactly?
On the Stew Mac templates there is no stud ledge, but the saddle area is at one thickness and they have a second template for routing a deeper recess just for the back end of the bridge, here you can see the two different templates that overlap to create a recessed FR,
That works but if the saddle section isn't routed deep enough the plate could hit the bottom of the route, with the stud ledge there is less chance of that happening as the route is at a shallower depth for less time before the deeper recess.
Or do you just route the whole thing at the full recessed depth and just not screw the pivot bolts into the body studs as far to create the same bridge height?
This is the simplest way but if the pivot bolts aren't screwed in as far they may wiggle a bit more than if the studs were at a shallower depth,
Is it a small enough difference not to worry about it?