If you're selling someone a company, surely you would just sell them the merchant account and company bank account as well, no? Did they sell the application but not the company?
How common are the two scenarios? A lot of YC companies are created with one and only one thing, so I guess you can sell the whole company. Other kinds of companies might have more products, and sell the product off, rather than the company. Does it really matter much one way or the other?
That's a fair point. I think it would matter only when the company in question has decided to share common tasks (like a bank account, or even a user database) across all of their projects.
Quick decoupling or forced encapsulation of projects seems to be a consideration that should be built into a company with more than one product.