ITK’s transformation infrastructure is very limited (there is no support for dynamic non-linear transformation chains with arbitrary combination and real-time inverse computation), so it definitely cannot replace VTK’s resampling filters.
I don’t know what you mean by native scanner space. DICOM uses LPS for defining image position and orientation. Probably each device has some internal coordinate systems but normally you don’t have access to that from outside.
The main goal of the activity described above is that you can we should be able to remain in patient space. Eventually, all VTK filters will be updated to work well with arbitrarily oriented images (or they will report that they require axis-aligned image input).