Based on the <Extensions>
element of the WP8 Onenote app it seems only *.one and *.onetoc2 file extensions are supported in the current version. That makes sense connsidering *.onepkg files are templates to create new files but app2app file extension support is currently limited to read-only scenarios.
<Extensions>
<FileTypeAssociation
Name="OneNote file"
TaskID="Default"
NavUriFragment="CmdLine=-s "token:%s"">
<Logos>
<Logo Size="small" IsRelative="true">OneNoteFileIcon.small.{ScreenResolution}.png</Logo>
<Logo Size="medium" IsRelative="true">OneNoteFileIcon.medium.{ScreenResolution}.png</Logo>
<Logo Size="large" IsRelative="true">OneNoteFileIcon.large.{ScreenResolution}.png</Logo>
</Logos>
<SupportedFileTypes>
<FileType ContentType="application/onenote">.one</FileType>
</SupportedFileTypes>
</FileTypeAssociation>
<FileTypeAssociation
Name="OneNote notebook"
TaskID="Default"
NavUriFragment="CmdLine=-s "token:%s"">
<Logos>
<Logo Size="small" IsRelative="true">OneNoteNoteBookIcon.small.{ScreenResolution}.png</Logo>
<Logo Size="medium" IsRelative="true">OneNoteNoteBookIcon.medium.{ScreenResolution}.png</Logo>
<Logo Size="large" IsRelative="true">OneNoteNoteBookIcon.large.{ScreenResolution}.png</Logo>
</Logos>
<SupportedFileTypes>
<FileType ContentType="application/onenote">.onetoc2</FileType>
</SupportedFileTypes>
</FileTypeAssociation>
<Protocol
Name="onenote"
TaskID="Default"
NavUriFragment="CmdLine=-u "%s""/>
</Extensions>