I'm not sure if BS is designed to convert a partial mash recipe into extract. That might be why the pale dme disappears, although I suspect it's just including the pale dme within the wheat extract calculation because, as others have stated, wheat extract tends to be 50/50 wheat and pale malt.
I suspect BS also considers acid malt a mash adjustment, rather than a flavor adjustment, so that is why it is not carrying over into the extract recipe. If you steep acid malt you'll get the acid and I suppose some of the barley flavor out of it but beyond the acid on the exterior of the grain you need to mash acid malt to convert the starches into sugar. If you don't mash then you generally do not want to add grain that requires mash conversion to your steeping grain.
You could check on the beersmith forums, I'm sure those folks could verify this info is correct.
If you want to toss up the ABV 0.4% I'd just include some table sugar in the boil to get you to where you need. It may require slightly increasing the bittering hops to keep the IBUs.