I'd say that's because they're the people who talked to you on the phone, and a major part of their job is to be a liason to walk businesses through their rules. You should look at them as someone who can inquire within the organization on your behalf, rather than someone to challenge the competency of.

Such people can be pretty handy. Yes, I know, it's frustrating that they don't understand a lot about your business, but again, their job is communication, so it probably just means they don't have experience with talking to projects like yours. Why not educate them so the next project down the line has an easier time?

Finally, the people who actually set those policies are very likely experienced and I'm going to guess are also pretty competent. If you are reasonable and have a positive attitude with the people you speak with on the phone, you might get to talk directly with such a person. I personally think that would have probably been the easiest way to resolve this matter.

But so what? You knew what sort of firm they were before you started this project, and while they may have their heads under a rock it's not really their responsibility to understand every business model out there, or to explain all the many ways that people have tried to scam them. To be honest, I think you ought to have had a chat with your legal counsel before setting the ball rolling; given that Paypal has a reputation for being inflexible with merchants, you could have been better prepared in terms of either your business structure or finding out what documentation they'd want to release your funds.

What does the license of the software have to do with the risks involved? What is the special case that they didn't understand that makes your project a smaller risk? What are the exact mechanisms in place that will prevent the project from failing miserably in any of the myriad ways software projects routinely fail after most of the money is spend and trigger a non-trivial number of chargebacks?

That for example this is not a software project where people for receiving the software. For example the perk for the $4096 backer tier is

"In addition to the previous perks you and your logo will be the most prominently featured in our credits. You also get a custom feature / design theme per your specs (see the FAQ for some fine print). In addition, if you fly to Iceland we'll meet with you to discuss the implementation and then take you on a road trip through the Icelandic countryside, taste fermented shark and our traditional alcohol Brennivín, whilst we talking tech, politics and security."

That's a pretty expensive chat to have, even if it includes the flight. Yet, two backers were willing to pay that price. All other tiers have a similar relationship between price and value provided. This cannot be explained in a rational business relationship - a solid gulp of idealism is included here. That influences the risk of chargebacks - backers paid to see this project worked on, not to receive their individual copy of the software.

That last paragraph is I think they key people aren't getting about IndieGoGo and Kickstater. You aren't paying for goods or services when you fund something on those sites, you're essentially donating towards the development of something, and gambling that in the future you'll receive something. The expectation is that the company/people you back will make a good faith effort to provide what they've said they will, but there's no guarantee you'll ever actually receive anything.