Amiga OS 3.5 shipped in a box with a boot floppy.
OS 3.9 originally shipped as a jewel case. The assumption was, you were already running OS 3.5 thus having a CD drive configured on your Amiga, or you had OS 3.1 with a CD drive. It is very easy to create a boot floppy for OS 3.9 from the CD.
I keep my OS 3.9 CD inside the OS 3.5 box. Plenty of room in there.
