Future projection will be added in Autopano ( v3 not before because of some internal issue ). We will also propose a new solution for this kind of job in a separate product ( The prototype was showed during 4th Autopano User Meeting ). The idea is to be able to undistort local part of each images making an arbitrary multi-planar projection which is really nice looking. In any case, it will take some time for both to come out.
Now I use external program to convert panorama to pannini. But it's not good - I use layered PSD for editing and always to keep all my layers, including source layers, used for patch. Therefore I need good projection before editing, as output of render.
Pannini is important projection. Now I use it in 50% of panoramas
Be sure, it's really high on the priority list. Nevertheless, there are other projects for the moment that are taking our attention : Panotour 1.6, gigatiler and the release of the Girocam hardware. After that, we'll be back on autopano dev.