The only reason I can think of that DC might say not to re surface would be the danger of flywheel breakage.
If you cut off enough of it, it may weaken it. If it comes apart at high rpm you could be injured by pieces of it.
Some small time racers will turn down a stock flywheel for weight reduction. They cut off quite a bit of iron. This can lead to breakage.
I wouldn't think that cutting off just enough to true it up would be a problem but I guess DC does.
Stock flywheels are always on ebay and cheap too.