According to the documentation, regarding autouic:
If a preprocessor #include directive is found which matches ui_.h, and a .ui file exists, then uic
Issue mentioned in this answer is now resolved.
This worked in CMake v3.9.0-rc6:
set(CMAKE_AUTOUIC_SEARCH_PATHS your/folder/here)
See documentation of AUTOUIC_SEARCH_PATHS.
Update
A search path, CMAKE_AUTOUIC_SEARCH_PATHS, has been added to CMake version 3.9.
After further investigation, it seems like it's not possible to do. There is an open issue in their tracking system, but it is so far not implemented:
Add Search path for AUTOUIC