If the 0.6 is after you add the motor - then what is the stability caliber before you add the motor?
I've seen other folks ask this? I am curious why you would care what a rockets stability is without a motor? It doesn't fly without a motor...
Yes, that. (See Lake, we agree on something.

)
As for which matches the actual flight condition, with the cone or without, the answer is obviously that neither one does. One adds drag to the sim that's not present in flight, and the other leaves out stabilizing force that is present in flight. And that's why, if I an correctly reading his mind, Neil advocates doing two versions of the OR (or RS) model. One with the cone gives a better representation of the stability than the model without. Note the distance between the reported CP and CG. Then remove the cone, giving more accurate drag. Note the new CP position and move the CG forward so that the distance between CG and CP is the same as it was with the cone.
Does that perfectly reflect reality? Of course not, because the CP is in the wrong place and the moment of inertia is now wrong. But that will have much subtler and less important effects on the simulation results than the other options.
Remember, base drag doesn't really change the CP. The CP is the imaginary point through which the sum of aerodynamic lift forces can act to produce the same net result as the combined lift forces in their actual positions. Let me emphasize a key word:
lift. Base drag isn't a
lift force, so it doesn't, strictly speaking, affect the CP. What it does is provide stability, but by a different means. How much does it improve stability? Well, by about as much as the stability would improve if the CP were yay much behind where it
actually is. So we approximate the stabilizing effect of base drag by forcing the model's CP aft by yay much, but the factual CP isn't really any different with base drag than it would be in a magical world where base drag doesn't exist. What we've got with the cone in place is an effective pseudo-CP. And it's an approximation.
And here's another thing.
Base drag isn't the most important thing here. 0.6 cal is probably fine, and would be in that magical, base dragless world too.
Why 1 cal? If the CG is forward of the CP then the rocket will right itself and be stable; what does "marginally stable" mean? (As applied to rockets that is; applied to our average mental state it's an entirely different thing.)
The CP calculations performed by OR and RS, and by people using the Barrowman equations by hand, do not take body lift into account. Body lift will cause the (actual) CP to migrate forward with increasing angle of attack (AoA). The amount that it moves depends a lot on the tube's length. For relatively "normal looking" rockets it will generally not move more than one diameter. So if you've got better than one caliber static stability margin you can be confident that the CP will not catch up to the CG during flight. The thing is, when a rocket is stubby, the CP migration will be slight, and your 0.6 caliber margin is probably fine. A stock Mean Machine has a stability margin of - well, I don't remember, but it's a lot. It needs to be a lot because there will be a lot of CP migration with AoA.