Of course, there is no one person for whom it is possible to perform all 613 Mitzvos. This question is classic Shabbos Derasha fodder, and has been dealt with by countless Meforshim. Whatever the specific answer, the general idea is that it is possible to be considered as having performed all Mitzvos (and even rewarded as such), including those which can not apply to you.
In any case, you would make my point even stronger. If even the “Milayim” of K’lal Yisrael fall short of 613, there is no reason at all to infer that the pomegranate has that number of seeds.
See next post for a completely different theory about the whole pomegranate-Mitzvos connection.
By the way, Randomex: “Does anyone else remember being taught that Yosef’s dream was of bundles of wheat in a field, with all the bundles bowing to one bundle?”
This is precisely how the dream is described in the Pesukim (plus the detail that it was Yosef and his brothers who were bundling the grain). I assume I must have misunderstood you.