In SP13, there will be a new command in ASE Civil's Profiles ribbon tab:
The "Align Select" option provides a way to change the alignment used for profile generation without creating a new drawing.
Freedom to Explore
So essentially, you could use this new option to browse all the available profiles in the project from within a single drawing.
This could potentially boost profile reference file creation, especially in large projects. Simply select the alignment, generate the profile, SaveAs a new alignment, use the new command to choose the appropriate alignment and there it is.
Save it, then SaveAs and move on...
Small Collateral Benefit
Although I didn't design it this way, it worked out such that any branching or customization that you perform in a generated profile is saved. Even after switching to different alignments then switching back. Your edits are not lost in migration.