I think I have just discovered the answer.
By only modifying the number in External Loads - Gravity I have arrived at around the same increase in max stress. This would therefore suggest that the factor need only be applied to the gravity and it will feed into any externally applied masses but would like that confirmed but someone more knowledgeable than I please.
Force = mass * acceleration. Gravity is the acceleration in this setup. You have done it correctly by only increasing the acceleration. If you increased the mass also, you would be getting double gigged. I'd add that, assuming this is a linear study, if you analyze the design loads without adding the safety factor, you can just read the actual design safety factor right off of the results. That would save you a step.