Don't forget back when YC invested in AirBnB and Stripe that they only put in $20,000 for the 7%, which brings down your valuation quite a bit closer to something that might include AirBnB and Stripe as 10,000x exits.
As I understand it, YC has the right to participate in priced rounds at the same valuation as other investors to retain their 7% stake. That does reduce the return on their most successful investments (since the denominator is bigger), but it also causes those investments to make up a larger share of their portfolio, which helps their aggregate ROI.