After you did the SYS command you would be able to boot the new drive exactly as if it were the old drive. SYS copies the boot record/files of one drive to another.

If you were to do SYS C: A: you would get a bare-minimum DOS boot floppy.

To answer your question, yes. But as [I think] you said, you should do the XCOPY command and SYS command from within windows so the long file names don't get trampled.