Listen to what Graham himself says: if you have customers, nobody cares what your pedigree is. Most successful companies don't come through YC. Most funding sources --- top tier VC included --- don't come with real PR benefits. YC does. But it's not proven that you need it.
I am not sure how that is funny. After web applications started dropping like flys about 2000 I decided that I could build my own that would be just as good but without millions in venture capital.
If by "bootstrap" you mean "build an app in your spare time while holding down a full-time job in IT at Wells Fargo", you win the argument.
If by "bootstrap" you mean "build a company without funding", implying making payroll, I think you're nuts. It's at the very least incredibly scary to bootstrap a company.
The opposite is to get the money first, create a company, then build an application.
I would prefer the last one, but getting the money up front is really difficult for most people. Not because there idea but there connections. YC builds the connections, helps build the idea, and then puts it all together. So while YC is great, there will always be a greater number of people wanting in then there is room. So it is back to Plan A.
If you already have customers, you're doing YC a favor by applying.
There is one exception in the companies they have taken on but all the rest were not established and only a few looked like a sure thing (auction manager, photo editor, comments manager).