The marking of these rolls was actually intended at the outset to be
done very carefully.  Aeolian introduced the Metrostyle marking system in
1901.  It was their way of making a live recording available to the
roll-buying public in the days before successful hand-played rolls were
marketed.  Initially the rolls were metrostyled by staff, and later by
pianists, composers, etc.  It was quite simple to do with the gadgets
available.  If you go to my web site and take a look at the Electra
patents page you will see a gadget there for marking a roll as it
played (although Electra didn't actually make metrostyled rolls):

  http://www.themodist.com/ 
  (go via Music Rolls / Roll brands / electra)

At Aeolian there was a pantograph system where visitors to the factory
recalled seeing girl operators following the red line on a master copy
which the pantograph ink marking machine would make 20 copies or so at
a time.  It was paid piecework, which meant that when the manager wasn't
looking the girls would just waggle the levers to get through as many as
possible.  This is why many metrostyled rolls have often meaningless
markings.

Look out for the early 65-note versions: these have the most accurate
copying.  They took care in the first few years.  In the 1920s they used
a stenciling system to put the red lines on, which improved accuracy
again.

As to the roll of Sousa marked by the composer, this is indeed correct and
it is an "Autograph Metrostyle" roll.  There is a long article all about
it at the Player Piano Group web site, with lists of artistes who made
recording via the red line method: http://www.playerpianogroup.org.uk/ 

For all the ups and downs, the Metrostyle system can produce perfectly good
results if used as a guideline.

Sincerely,
Adam Ramet
Shoreham-by-Sea, England
http://www.themodist.com/