In an email exchange today, one of Beagle’s Summer of Code students pointed me to this page in the Epiphany extension documentation, which states:
Epiphany extensions are classified as derivative works of Epiphany, which means they must be licensed under the GNU GPL.
Assuming the extensions are developed by using a well-defined published interface and not based on existing GPLed code, I’m having a hard time seeing how they could be considered a derivative work. The interface itself — even if it is learned from a header file — is not enough to create a derivative work; otherwise Linux could be considered a derivative work of Unix rather than (to a certain extent) a clone of it. Because of the clean interface separation, they are more like GStreamer plugins than Linux kernel modules, and should be licensable however the author chooses.
Now, Epiphany is GPLed and since extensions run in the same process space they would have to be a GPL-compatible license, but any compatible license, like the X11 license, should be fine here.