AFAIK most manufacturers don't sell their regulators with Miflex hoses. However, most dive shops (middle men) will be glad to add in the cost of an upgraded hose and sell you the reg with Miflex on it. You don't have a middle man involved when buying deep6, you're buying direct from the manufacturer.
Also, there's a potential problem from a manufacturers perspective in shipping products with Miflex preinstalled. Miflex hoses have a finite lifespan. That's not controversial, the manufacturer of Miflex will tell you that themselves. It's 5 years. The clock is ticking even if it's new and in the box. If a regulator shipped with Miflex and then sat in a dive shop's inventory for 4 years before it sold either the dive shop has to eat replacement cost or the customer is getting screwed. Neither situation is desirable for a business.
That said, I also like Miflex hoses. I have them on all my regs except when diving with a long hose.
Miflex solved the "chafing" problem by creating a "tech" hose.. that's basically a Miflex hose with a resin coating. It's almost as flexible as regular Miflex, but won't hurt your neck. Miflex still isn't suitable for long hose in my opinion because Miflex kinks very easily - even when pressurized.