The problem is that it makes it clear that the market for third-party software is completely at Apple's pleasure. If Apple chooses not to issue me a Developer

The problem is that it makes it clear that the market for third-party software is completely at Apple's pleasure. If Apple chooses not to issue me a Developer ID, they have effectively removed 95%+ of my market. If this is because I distributed malware, that's reasonable. But there are a lot of other reasons why Apple might choose to revoke a Developer ID. (Think pressure from the state, for one.)