Also submitted via feedback hub with the relevant log and manifest. This post contains additional information after further analysis.
MixTex installs some COM. The packaging tool appears to not detect the duplication when creating the manifest, resulting in this:
<com:Extension Category="windows.comInterface">
<com:ComInterface>
<com:ProxyStub Id="8be9f539-b949-4c7b-991c-db6c6f737ec7" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-core-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="8be9f539-b949-4c7b-991c-db6c6f737ec7" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-core-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
<com:ProxyStub Id="78ad6d5e-2972-412f-9a58-e57ddde739b2" Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-packagemanager-PS.dll" DisplayName="PSFactoryBuffer" />
I also find a duplication issue under the Com:Interface entries of the package:
<com:Interface Id="49c9f0b8-3df6-4bba-9dcd-3fe289df95d8" ProxyStubClsid="8be9f539-b949-4c7b-991c-db6c6f737ec7">
<com:TypeLib Id="392bfc08-8cd2-487f-87ee-b2da213bbd20" VersionNumber="1.0" />
</com:Interface>
<com:Interface Id="49c9f0b8-3df6-4bba-9dcd-3fe289df95d8" ProxyStubClsid="8be9f539-b949-4c7b-991c-db6c6f737ec7">
<com:TypeLib Id="392bfc08-8cd2-487f-87ee-b2da213bbd20" VersionNumber="1.0" />
</com:Interface>
And duplication for Com:Typelib:
<com:TypeLib Id="392bfc08-8cd2-487f-87ee-b2da213bbd20">
<com:Version VersionNumber="1.0" LocaleId="0" LibraryFlag="0" HelpDirectory="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64">
<com:Win64Path Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-core.dll" />
</com:Version>
</com:TypeLib>
<com:TypeLib Id="392bfc08-8cd2-487f-87ee-b2da213bbd20">
<com:Version VersionNumber="1.0" LocaleId="0" LibraryFlag="0" HelpDirectory="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64">
<com:Win64Path Path="VFS\ProgramFilesX64\MiKTeX 2.9\miktex\bin\x64\MiKTeX209-core.dll" />
</com:Version>
</com:TypeLib>
The Com:ComInterface element requires unique ID fields in the ProxyStubs (and the others) causing the tool to fail in MakeAppX.
