I think I asked years ago about duplicating these,
 but is there a practical way to do that with just a 1541? 
NO!
NO!
NO!
What you can get PRODUCED by a normal drive, is a NORMAL disk.
What you can get PRODUCED by a normal drive, is a NORMAL disk.
What you can get PRODUCED by a normal drive, is a NORMAL disk.
You CAN NOT produce an alignment disk using a normal drive with a normal
controller.
You CAN NOT produce an alignment disk using a normal drive with a normal
controller.
You CAN NOT produce an alignment disk using a normal drive with a normal
controller.
  I mean, if you align a drive using a scope with the
disk,
 then duplicate it, how reliable is that copy for alignment of other drives? 
WORTHLESS.
What you create with the normal controller with normal drive is a NORMAL
disk.  IT IS ABSOLUTELY NOT AN ALIGNMENT DISK!
A "digital alignment disk" is a disk produced using a special drive, that
DELIBERATELY has sectors written OUT OF ALIGNMENT, in order to see which
sectors (HOW FAR OUT OF ALIGNMENT, AND IN WHICH DIRECTION) can be read by
the drive.  Doing so provides a "reasonable" level of measurement of how
far out of alignment the drive is, and which direction.  A disk written
with a NORMAL drive is aligned for that drive, and can NOT check anything
except whether a given drive is close enbough to alignment with the drive
that created that disk to be able to reade it.   People who think that
THAT is "correct alignment" really don't give a shit whether the drive is
accurately aligned, or where within the range that succeeds in reading
THAT disk it might be.   It is "close enough" to be able to read/recover
disks written by that drive; it is NOT acceptable for writing disks,
particularly for distribution, or even exchanging with other people who
have been doing the same, and have drives ELSEWHERE in the range that
reads THEIR "known good" disk.
It is a BAD, STUPID IDEA!
If you take a yardstick, and use it to make marks on a stick, and then use
that stick to make marks on another stick, and continue to use each stick
to make the marks on the next stick, HOW MANY sticks can you make that you
would claim are accurate?
Disunirregardless of the alignment of the drive, ANY disks created by that
drive are aligned to that drive - they are ABSOLUTELY NOT a graduated
and calibrated series of misalignments - they are ALL aligned to that
drive.  Yes, "piracy" programs (blow it out your ass if that offends you),
can make a "copy" of the disk.  But THAT "copy" is aligned to that
drive,
it is NOT an alignment disk, and is absolutely totally useless for
checking alignment of anything.
An "analog" alignment disk can not be created with a "normal"
controller/drive combination.  Instead of "normal" digital data/sectors,
it has SPECIAL tracks written by special hardware. They are analog tracks,
containing signals for testing drives, and a normal drive/controller can
read them, but can NOT write them.
So, anybody who claims to "duplicate" an alignment disk with stock
hardware, disunirregardless of what software is used, is an ignorant
asshole.