It is now possible to override main.m and Project-Info.plist by putting the files in the special folder.
I have tried to upload my project to itunes-connect. The main.m for
B4X:
#PlistExtra: <key>UIBackgroundModes</key><array><string>fetch</string><string>remote-notification</string></array>
isn't accepted. It is only possible to delete the main out of the special-folder and use the one under the projects-folder of b4i.
The normal main.m is accepted by itunes, when it is in the special-folder.