What if you added something like:
```scala
sealed trait HeaderMode
case object NoHeader extends HeaderMode
case object WithHeader extends HeaderMode
case object WriteHeaderSkipOnRead extends HeaderMode
```
Then the code be clear (the boolean is a bit confusing to me).  We could default to NoHeader.

Give that try.

Also, the next version of scalding 0.9.0 we will have many small binary changes (very few source code changes).  So, it might be easier to just merge this in that cycle (starting soon).