In another thread, the comment was made that it's the same DSP code, so same input will result in same output. However, your A/D converters, etc in your interface are possibly different to the ones they use in the hardware Helix, so that could make the input to the DSP code slightly different.
I only plan to use Native for recording, and don't have a Helix, so I don't need it to be identical. If you want to interchange presets between Helix and Native, then it possibly matters more.
Cheers
Malcolm