Nope.
Once it's balanced, the rotating assembly (damper, crank, pistons, rod, flywheel/flexplate) all need to work together. Stock 400 SBC's are 'externally balanced', and all other stock SBC's are internally balanced. In simple terms, all that means is that the stock 400 damper and flywheel/flexplate have a counterweight on them (externally balanced), and the other stock SBC's do not (internally balanced.)
Since you said it was a 406, that means it's been rebuilt, so it's not stock any more, and it could be a mix of stuff, so you can't just assume it's using a counterweighted damper and flywheel/flexplate.
The only thing you have to worry about when switching from an automatic (flexplate) to a manual (flywheel) application is that the new flywheel is balanced the same as the old flexplate. If the flexplate is a neutral balance type, then you should use a neutral balance flywheel. If it's a counterweighted flexplate...you need a counterweighted flywheel.
Beware though, "balanced for an automatic" doesn't make any sense (should be internally or externally balanced) and might mean the seller is full of crap.