3.5 shipped in a box, versions before that either came in a bag or a white leaflet, with a seal.
3.1 came in a box also (white cardboard, about 12" long, 5" wide, and 3" deep, containing manuals, disks, etc). I just don't have it anymore, and couldn't find a picture to link to.
From memory it certainly had "Amiga" in the newer typeface, but I think it may have just said Amiga v3.1 (with the v3.1 in a much smaller typeface).
Not that it matters at all in the scheme of things, it's just worth pointing out the distinction when people try to blur the distinct line between Amiga OS 3.x (developed for Amiga computers) and AmigaOS 4.x (developed for AmigaOne computers). :-)
@Nicholas
I'm pretty certain they also got the rights to "Amiga OS" - just not "Amiga" - which basically got kicked into the long grass wrt ever being used to name a computer running an Amiga-like operating system ever again.