Which of the license restrictions actually poses a challenge to anyone who is trying to further the goals of the mailpile project? The emphasis on security and not trusting the server or service providers already precludes integrating it into a closed-source product.
It hinders growth paths and stops reuse that would lower the bar for spreading secure e-mail support.
AGPLv3 has license restrictions that are unacceptable to many or maybe even most companies, and secure company e-mail would be a great first growth application. Even for personal use easy 3rd-party deployment by hosting providers would be desirable, but AGPLv3 may be of concerns for these hosts for a fringe-application.
AGPLv3 also prohibits code-reuse in most contexts, so it makes surprising reuse of sub-components less likely. Stopping this reuse is a shame since it could have reduced the bar for implementing secure email support in more e-mail clients.
In email clients with either more permissive or even proprietary licenses, where those Mailpile most wants not to use their source (evesdropper backend email services like gmail) can then use their work to enhance their user experience without providing their users the software freedoms they enjoyed when modifying mailpile or a permissive fork of a permissive piece of it.
Who needs an evesdropper backend when you can just watch the network traffic? The messages back and forth are just data, and an MITM proxy is invisible. The end result being that the company has a face of providing privacy, but knows every little thing about you.