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It really means stages of engine upgrades. I can only speak for stage 1 because that's all I am familiar with: Stage one is high flow air cleaner, high performance exhaust, and fuel delivery modification, as in a fuel management solution (Power commander, SERT, etc) for FI, or carb jet changes (richer) for carburetors.
That was an interesting link to read but I don't know anyone that has a Stage 3 setup that is "blueprinted".
Maybe it happens but my stage 3 runs just fine as a complementing system but I'll be stuffed if I would ever spend $$ on a "blueprint" for a moderate stage 3 build....