I don't know the answer to this question (factory or not) but, whenever I pass through Southport (CT), I stop at Hansen and Hansen (
http://www.hansenguns.com/). They've got an amazing variety of guns for sale and are very friendly. When talking to the proprietor 3 years ago, he commented that he'll occasionally get a Ruger firearm from an employee or ex-employee in an unknown caliber. He also buys gun collections from Ruger employees with all the same serial number.
Sometimes they are experimental and sometimes just something that an employee cooked up (or ordered) using available components. Perhaps this rifle is one of these, or it could just be a re-bore or re-barrel.
Question - If it is a one off rifle made at the factory for an employee, is it a "factory rifle", a custom rifle or, just a mis-matched rifle?