As the proud owner of a "Franken-Reg" rig, I thought I might weigh in here!
The set that I currently dive is:
First stage: Apollo with the Bio Filter
Primary Second: Atomic Aquatics Titanium B1
Octo: Apollo Prestige EX2000 (on a Mares hose!)
When we decided we were ready to buy, the owner at my LDS gave us a quick course on regulator anatomy (piston vs diaphragm) including pros and cons of each as well as explaining his personal preference. He then gave us a walk through of the different regs available. When we started talking about what we wanted, he offered us a nice deal on the setup above. As he explained it, the technology is the same, the fittings and sizes are standard, and how would the air know if it is going through one manufacturer's equipment or another's?
Bottom line, if you like the features of one company's first stage and another's second, there is no conceivable reason you couldn't buy them separately. Most shops don't display them that way, but if that's what YOU want to spend YOUR money on then so be it. You are the customer, after all.
Personally, I couldn't be happier with the equipment I got. And, in case any skeptics were wondering, the Mares Abyss was the "shop special", not the Atomic or Apollo