Ron Burgundy
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A small amount of disc runout will not cause brake pulsation. Calipers have slide pins designed to cope with this sort of lateral movement.
Two things cause runout (that come to mind) - thickness variation and pad material deposits.
Your pulsation was likely caused by brake pad deposits on the new disc. If new brake components aren't bedded in properly there's a risk that a very thin layer of brake pad material sticks to the disc surface, causing a grabbing or sticking feeling like pulsation. Google it.
Good quality brake component materials are supposedly matched to minimise any chance of this happening (OEMs go to great lengths to ensure this). Mixing and matching brands and materials is where I've seen this most.
If there is an amount of runout outside of acceptable spec, at its highest point the pads will build deposit. This will then result in pulsation...