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Setting it with the car off and pump on makes no sense to me.
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Why wouldn't it make sense? You'll have vacuum in the cylinders and the injectors opening constantly (meaning that the system is not closed) with the engine running, not to mention working around a hot engine can be painful sometimes.
Also, with the engine running and the vacuum line off, the engine isn't going to be idling properly anyway since fuel pressure will be too high causing it to run richer than it should.
There is absolutely no reason why the engine would need to be warmed up to set your fuel pressure. The FPR is basically a pressure relief valve that you set to open at a specific PSI.
You'll get better measurements, its easier since you don't have to disconnect anything, and it will be safer.