Patrick, it appears from the posts above that you believe the .30-03 case has a longer head-shoulder dimension than the .30-06. However, the only significant dimensional difference between the two cases is the length of the neck. Headspace dimension is the same for '03 and '06. Consequently, there's no need to back off the sizer die (or to refrain from using .30-06 ammunition in a .30-03 rifle). Also, the exercise you describe with the marked rod will not provide any useful information for differentiating between '03 and '06 chambers.
FWIW, the .270 Winchester chamber shares its headspace dimension (SAAMI max 2.0587" to .375" datum) with the .30-03 and .30-06 but does, indeed, have the extra neck length of the '03.
There are several practical ways of measuring chamber length, the simplest being the insertion of a greased 00 buckshot atop an empty case into the chamber and closing the bolt. The chamber mouth will leave a distinct impression on the buckshot that can be measured to give total chamber length from the bolt face. Examples below are in 7.5 Swiss, but the method works the same with US .30 caliber rifle chambers.
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