Ay caramba, Ari, that's a lot of questions. Break it down for me so it's easier to address.
You are not mistaken about the instructions given by the maunufacturers of lead hardness testers. But your interpretation might perhaps be subject to an understandable misapprehension. Consider that the instuctions are guidelines and not explanations.
The reason that a small flat is advised is so that the underlying material is not affected by cold working. A small flat cut into the surface will suffice for the test, but a larger flat may result in more cold working, and since the test is one of small degrees, any cold working will confuse the results.
The reason that the base is not recommended for hardness testing, is simply because that area already
has been subjected to cold working when the sprue was cut, and so it is not a suitable area for testing.
Cold working causes the indentation to be artificially deepened and widened. Since the test involves tiny measurements and magnification, any degree of work softening will skew accurate test results. A file can work soften the material under it, so it's easy to see that a small flat filed carefully is better than a more extensive flat.
You may wish to read more about the physical mechanism that causes the increase in hardening upon quenching an appropriate lead alloy. It is called grain-boundary strengthening or Hall-Petch strengthening.
http://en.wikipedia.org/wiki/Hall-Petch_Strengthening
http://www.chemie.de/lexikon/e/Grain...strengthening/
Here is a short article on the subject as applied to bullet alloys:
http://www.lasc.us/WiljenArsenic.htm
I do not wish to dodge any of your questions. After you have read-up on Hall-Petch strengthening, please address your questions to me again (maybe a few at a time, so I don't have to type-out a book) and I'll be happy to shed what little light I can.
Good shooting.