It says all 3 but does that also include the afterstory and Act 3?

No. We planned to include an “All Five” where you play everything from 1, 2, 3, Afterstory, Finale. But because of how long it may take for one to actual run it. So no, “All Three” is only the main FNaFb 1, 2 and 3

But what if 'I' did an All Five run?

nevermind, i see we have updated

We sure have