autoUPX is my baby, so my reply.
6.1. There is still mistake in my_UPX-Able_DLL.txt (instead of Diskcopy.dl_ there is Diskcopy:dl_ and as a result Diskcopy.dll is not UPXed).
6.2. The my_UPX-Able_DLL.txt is still ignored and 28 dlls are not UPXed:
6.3. Three biggest dlls in WinSxS folder (Mfc42.dll, Mfc42u.dll and Comctl32.dll) are not UPXed.
6.1: Im going to fix it ASAP
6.2: I used the list Oscar in the 911CD forum published.
Maybe that inside the Standard project files can be UPXed which in BartPE or Reatogo cannot.
To be on the safe side i did not include other files than those from the list.
The my_UPX-Able_DLL.txt file is not longer supported. To include files of your choice into UPXing you have to define them in ProjectInfo.ini (see here or click the Help button in autoUPX.Script.
6.3: Same as 6.2.
If I get some more posts asking for it, I'll include the above files in the UPXable internal list.