Why? Hypothetically someone could take a standard loan and use that. That would be cumbersome, and sometimes impossible, but it wouldn't require a "super high" interest rate.
They both work as hard and they both share the same risks. If they fail, the IOU still applies. One just happen to have more money stashed away.
Both partners might work as hard, but they don't share the same risks. One has put X thousand more into the business, and they should be compensated for that additional investment. The fairest way to do that is to consider what terms you'd find reasonable on an investment of similar risk.
I re-read the entry and it isn't clear to me if Spolsky thinks the IOU should be there even if the company ceases to exists. Me and my two co-founders had a similiar arrangement, albeit with very small amounts, and after the company died they paid me back the unofficial loan. We were all students and I happened to have some more disposable money for initial investments (under $3000 though).