OK, Kevin, I think I see what you're talking about. Hopefully, Martin or Brian (Pork Belly) will chime in on this one. My take is that, since you are wet brining (meat submersed in liquid), with an equilibrium brine, the percentage of nitrites doesn't matter; the entire solution will equalize. In large cuts, like a ham, you would inject the same brine into the meat, especially around the bone. Given a long enough brine time, the solution will eventually reach equilibrium throughout the meat. Make sense?
From my rudimentary understanding of ham making, I believe you are referring to injecting brine, but not submersing the whole piece in solution, right? These are two different animals, that essentially achieve the same results. The difference being, is that the equilibrium brine will be repeatable, very predictably.
As far as the 6.25% calculation - that is the percentage of nitrite in the #1 curing salt, not the desired percentage. If you inject the solution, with the amount of #1 from the calculator, the ham will get cured all the way through.
Someone please correct me if my assumptions are wrong!