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It's unlikely that this would cause a problem. The reason the car rental company would want to see your passport is that it's picture identification. When you sign the rental agreement, the fact that you're standing there is sufficient for them. The fact that the signature doesn't "match" is not relevant.
If things were to ever get to the point where you were asked in a court of law whether you signed a particular document or not, it's either a "yes" or "no" answer no matter what the signature actually looks like.