Benta:
It's possible that warming up with an erection might be better, as the tissues in your penis - including the tunic and smooth muscle - will be stretched to their max. That said, I haven't heard of too many men warming up that way. . . Perhaps you're onto something?
Regarding your "minor discomfort" - what is it exactly that you feel? Is it just a soreness? Does it go away by the second rest day? Also, what are your PIs like?
And you're welcome for the guide

Glad you could find it useful.