I'll probably buy some Winchester defense ammo to use as a benchmark which means the cases will likely be nickel plated. I'd rather use regular brass for my loads. Will it matter?
Yes, it will matter. Waters would buy factory ammo, break some down, deprime, then reprime and load his handloads in the factory new brass, with very similar bullet, and very similar powder, and use a chronograph to check velocity, looking to get a similar velocity at the same case head expansion, assuming that meant similar pressure.
If you use different cases, it's meaningless. If you use the same cases, but the "benchmark" was shot with factory new, and your reloads with cases that have already been fired once and resized, it matters. If you didn't guess the factory powder closely enough and get a powder of a significantly different burn rate, it matters. If the factory ammo was .355 124gr JHP and your loads are .356 coated lead, it matters. Or bullets of a different weight, it matters. There are many differences that can matter.
THEN there's the question of what it accomplishes. It's not going to protect you from anything. Yes, people following safe loading practices occasionally manage to find their way into over-pressure loads anyway, but the causes of those over-pressure rounds aren't things this Waters technique would protect you from. Published LOAD DATA protects you from accidentally going higher and higher until suddenly you're in dangerous territory without knowing it. Just follow load data.
It could be an interesting exercise for the sake of the exercise, but it's not going to be useful. It's duplicating a protection provided to you already by published load data, and not as reliably.