This might be a new way of thinking about this, but, technically, the player IS on a penalty.
Note: This assumes the rule is that a player needs to be at his seat before the first card is dealt.
Since the player was not at his seat at the required time, he is disqualified from that hand. I.E. He is not allowed to play his hand even if he returns before the action would have gotten to him.
The penalty lasts for the duration of the hand, which includes the misdeal and re-deal.
When using the last card dealt rule, I'd allow the player to play the hand if he returns before the last card of the re-deal, even though that allows for the dealer-player collusion I described above.