Unless you are looking to shoulder up the barrel like a Remington you're greatly over thinking this. The beauty of the Savage barrel nut is that the headspace is adjustable. As such the only measurement you need to worry about with your barrel is how much the go-gauge protrudes from the breech, which should be 0.120 to 0.125" according to factory specs. Most pre-fit barrels I have received were made closer to the 0.125" mark to allow for some wiggle room. Again, the nut allows you to adjust it to match your bolt head depth so it's not as critical as your making it out to be.

So as MI223 pointed out, your zero clearance 0.109" measurement + the standard 0.1" minimum clearance = 0.119". Likely your bolt head or receiver face is short 0.001" (again, within a tolerance range) which would get us back to the 0.120" reference I gave above. The 0.006 he referred to is adding that missing 0.001" to the factory allowed 0.005" tolerance which gives us the 0.120-0.125" range previously mentioned.