My feeling is that if you submit a card in a holder, you're doing it with the knowledge that the grader can't see the edges, and can't examine the card as close up as they could if the card was raw. As such, your grader might go a little more conservative.
I have no concerns that PSA or SGC are biased against one another's holders. They want the cards IN their holders - not out of them.
-Al
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