That example only says 3% margin is better than 2% margin, not whether the hypothetical process yields better results than a bond paying 4% (or whatever). If the said process takes exactly 1 year to complete, and requires all the inputs to be provided upfront, then its margins can be directly compared to bond yields, but businesses are rarely that simple.

the bond example is a return on your money, the profit margin example is a return on other people's money.