Here's my take on the matter. If you want it to turn into a group of flip-flops, it can become memory. If you want it to be an Arithmetic and Logic Unit instead, it can switch to that in the middle of your program. Quantum pulse elements are so much faster and more convenient than other forms of computing technology that the old silicon stuff has become quite obsolete. With the universality of quantum pulse elements, you have access to processing that's as parallel as you want it.
All programs are compatible with other computers, as long as the computer is big enough to run it.
Programs from older computers can easily be run on an emulator. Naturally, programming and debugging with such elements is incredibly difficult without computer assistance. The computing environment of Shadowrun is a descendent of the applet-filled Java world currently growing on the Internet right now. Naturally, when it gets converted to text for a paper sourcebook, you wind up with the usual posts we're familiar with. This is, by modern standards, horribly wasteful, but memory and storage are cheap, and the same phenomenon that makes Microsoft Word take up 30MB on your hard drive today hasn't gone away.