I have no authoratative knowledge of the situation, but it may be that each and every of the PRO-100 printers are packed with a set of cartridges which are marked "setup" on the label, while the retail carts do not have such a nomenclature.
But to reiterate: The 'setup' carts are indeed identical to the retail variants
with exception to the top label. Included carts are labeled "setup" while retail carts are not.
That is the only difference in terms of physical properties including size, construction, weight
of empty/full...
If there are any doubts, simply search the Pro-100 and CLI-42 threads in the Canon section
of the PrinterKnowledge forums.
The only difference which has been suggested is that chips on "setup" marked carts
may not allow use of Canon's Image Garden software if reset, but there seems to be
no conclusive agreement on this.