The difference is that I think the fragmentation is permanent this time. Binary compatibility is far less important than it was in the floppy disc era -- the Internet is where the action is, and HTML, Facebook, Flash, others that are fading and more that will come along are the platforms that matter. As Sun used to advertise, "the network is the computer."
I think you have really nailed it. In the PC era, hardware became a commodity, but operating systems were not. Operating systems were closed and proprietary. Microsoft's closed OS dominated on commodity hardware.
But today operating systems are a dime a dozen like hardware. Fragmentation is not an obstacle as long as your platform connects to the network and just works without annoying problems. Portability is the important factor today. Your Internet device just has to work without a lot of hassles. I don't want to be a systems administrator. I just want the computer, phone, laptop, netbook, tablet to work and connect to a lot of other devices with ease of use.