You bring up some great points for manually cleaning up your models there. In the mean time your bust will have a resting plate - with a bunch of flat polygons. Use those as a "lay flat" to reorient it in the meantime. Slicer software typically has this (control+l ), but id imagine better software would too.
Once the orientation data is imported, it could be treated optionally like a normal layer - when you view iys transform and rotation it would have your preapplied rotation (from your head orientation when you did a copy to clay like you do currently).
You could then zero out these to get the models natural position.
This made me think too - often i may get trouble where i translate or rotate a model by accident and find out too late after doing heaps of steps or saving and losing the undo chain
These options may be too complex ui wise but:
A way to reset rotation to stock.this is because a created layer inherits your head rotation at layer creation doesnt it?
A way to reset it back to a user defined point.
Perhaps these could be hidden in a option click on the lock icon on the layer panel? I can understand how tricky it is to add functionality without confusing a new user!