It's "possible", but I think it's not a priority yet. It looks you want a full affine matrix transformation available. It seems it would be mostly a matter of adding a few more boxes to the GUI. You might try this yourself using the existing Nudge plugin as a basis for the code. Overall I have found the Nudge plugin useful for rough alignment, but it's really difficult to judge by eye which direction is best to get decent alignment. It's only after you get to a good alignment when you see, aha, there is a good alignment.

It might be the align_epi_anat.py script might line up your data better than you could with this proposed tool. Another choice would be the 3D tagset align plugin to mark corresponding points and then align with 3dTagalign. Try these, and let me know how they work for you. If you have some sample data, you can upload the datasets (using the Upload Data link on the left), and I can take a look.