Actually all the military stuff is governed by MIL-HDBK-516. They don't explicitly specify a SF when they release the RFP. The whole process is extremely tailorable to the specific aircraft being designed, meaning there are no hard requirements just vague criteria like "Verify that the airframe is designed such that ultimate loads are obtained by multiplication of limit loads by the appropriate factors of uncertainty. Also verify that the ultimate loads are used in the design of elements of the airframe subject to a deterministic design approach." (MIL-HDBK-516B, 5.1.5)

That criteria is used as the starting point for negotiations between the aircraft designers and the airworthiness certification offices. Not all criteria listed in 516 are applicable to all aircraft so the first task is to go through the document and determine what is applicable and what isn't. If a criteria is found to be applicable you can't modify it in any way, but you can enact a standard to fulfill that criteria. These standards are the primary source of negotiation between the certification offices and the designers. For example, a typical standard for criteria 5.3.3 (Stresses and strains in airframe structural members are properly controlled...) would be something like a SF of 1.33 for cast parts, 1.15 for fitted parts (if not demonstrated by static test), and 2.0 for bearings for elements with relative motion. However if an aircraft manufacturer comes back with a new process for casting a part that reduces foundry quality control problems and can prove through testing that they have a more accurate construction method thus reducing the need for a factor of safety, then they'll most likely get a reduction on that standard.

Anyway, long story short:

None of the military requirements are set in stone. The standards are negotiated with military technical area experts (TAE). From that the designers submit an Engineering/Data Requirement Agreement Plan (EDRAP) and use that document to outline all the analysis testing and evaluation needed to be done. Since the testing and evaluation is a huge cost driver for the developer they want to reduce the number of tests performed on the system. Each test creates an artifact that is submitted with the agreed upon EDRAP as well as other documents (system safety outline, FMEA, etc) which are then sent back to the certifying authority who then determine whether or not all the requirements were met. If they have been, then a flight clearance is released for that design.

And that, in a nutshell, is the military airworthiness certification process.

The SF is actually prescribed for the majority of civilian applications. Since the MTOW of White Knight 2 is greater than 12,500 pounds it falls under FAR Part 25 for certification requirements. The limit load SF prescribed from FAR Part 25.303 is 1.5.

The article states it was actually a low speed taxi test, but I agree with your overall point. I don't think I've ever heard of them as "runway trails" only "taxi tests".

I don't want to seem like I'm implying that there wasn't any industrial espionage going on during the development of the TU-144 or the Bakinor shuttle, however there could be valid reasons those designs turned out the way they did. In aerospace engineering (and in other engineering areas as well) form typically follows function. So when you're using technology of the day to design either a supersonic commercial transport or a lifting body orbital spacecraft, you're going to find the optimized aerodynamic shapes look quite similar even when approaching the problem from two initial starting points.

Is it solipsistic in here, or is it just me?

The first part of her statement was "I can't trust Obama, he's not... he's not... he's an Arab."

Maybe it's just my interpretation, but could it be McCain's comment about Obama being a good man be directed towards the first part of her statement about him being untrustworthy and not him saying that Arabs can't be good men?