Coop,
I don't want to misread what you are saying as I am having a tough time following it exactly.
If you are saying that we can't use die markers to identify a specific variety as coming from a specific die or die pair, that is not accurate.
Take for example the 1972
Lincoln Cent Die # 1, every known example has a small fingerlike projection that was the result of a miniscule die gouge. It is seen from the edge going to just above the D of UNITED on the reverse. There are many examples of the use of die markers of this kind to authenticate a die variety and lead right back to a specific die or die pair.
Sticking with 1972 Lincolns for a moment, We can determine which die varieties were the result of doubling on master dies, for example because we see the same die markers and doubling on Philly and Denver coins.
So something like a raised spot or line caused by a die gouge can be used as a marker to authenticate a die variety.
I think there is some confusion as to using small die breaks, which are errors to ascertain whether or not a coin is a specific die variety. You can only determine die state by small die breaks found on a coin. So that part of what you mention is correct.
This time let's use the 1997 Doubled Ear Lincoln as the example. First it is important that people forget about the thought that these are not doubled dies and are the result of the often mentioned, but incorrect "well placed die chip" theory. They are indeed doubled dies.
There are markers and doubling that can be used to identify the obverse die. On the reverse, there are various die stages that can be noted based upon the size of a developing chip on the upper left of the Memorial building on the reverse of the coin. Some have no chip, some have a small chip and some have a larger chip. So the die markers on the obverse tell us the coin is a die variety and the chip on the reverse (or the lack of it) can tell us something about die states.
To recap, you do use die markers that are common to every example of a die variety but you can't depend on minor errors, like die chips to do anything but give us an idea about the stages of the die or dies used.
So, if that is what you meant, We are on the same page, so to speak.
Thanks,
Bill