By default Ti speeds up simulator builds by sym linking and not pre-compiling js, but for uploads to systems such as pieceable a "full" non-symlinked .app build is required.
Pieceable provided some patches for SDK 1.8 and 2.0. See: https://github.com/pieceable/titanium-patches but none since.
I think it would be a useful option anyway and would avoid having to patch.
Please consider adding a "buildfull" option to the ti cmd line build options.