Every Amiga came with an OS license, so if the system shipped with the Kickstart 3.1 ROM(s), it also shipped with a Workbench 3.1 license.
I'm not positive, but weren't sales of Kickstart ROMs tied to OS licenses at some point? In any case, the OS kernel is in Kickstart. The other bits (CLI, Workbench, etc.) are what come on the disks. These days, no one (apart from the vendor) receives any procedes from the sale of Kickstart/Workbench, and if you do place and order, chances are good you'll get copies of Workbench disks instead of originals. ;-)
Think of it like embedding MSDOS.SYS and IO.SYS in ROM and shipping COMMAND.COM (and MORE, XCOPY, et al) and Windows separately.
