(I'm deliberately reasoning from a diegetic perspective.)
I wonder if Penny looks like someone Pietro knew in his(?) youth.
One possibility is that Penny's looks are drawn from old memories or even fantasies Pietro had of someone Pietro had once seen and who Pietro'd subconsciously thought of as a "goal", or perhaps how he once pictured what his daughter might look like if he had gotten together with someone he knew in youth (why such a person isn't in Pietro and Penny's lives in the present is irrelevant to this topic).
Another possibility is that Aura carries a lot less of the person than one assumes. That Aura is the power of the soul, but not the soul itself, so a piece of someone's Aura might not have anything that would make the source identifiable. In other words, Penny's soul(once booted up, for which Pietro provided the energy) is hers and nothing about it says anything bout Pietro's own.
One more possibility is that there is someone on Remnant who at one point looked exactly like Penny does in V1. that it was Penny who saw (a picture of) someone and decided "I want to look like that" and then took it extremely literally. (Wouldn't surprise me if Penny took a question as "what would you want to look like" too literally and chose an appearance to mimic exactly, not realising she had room for modifications until she was already used to thinking of the copy as "her" and changing it too drastically started feeling wrong.
There's also how Remnant doesn't seem to have skin-tone based intra-human racism (xenophobia and anti-faunus racism), so that particular difference between Pietro's appearance and Penny's might not have any connotations(to the characters, exegetically there are questions) that wanting to dye one's hair a different colour doesn't (beyond it taking much more effort to do).
(Tangent, "Friend" started playing when I was writing this, which feels really fitting somehow.)
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