
After having checked that there is indeed no solution to solve that issue with any tool, I contacted Martin Wright and explained him our situation. He agreed to help, and made a set of console tools for conversion and alpha channel adding. I wrote a warpper for these tools that allow to operate them in batch mode.
As an initial test I have converted all P-3 textures from all MAIW packages and gave them to Gavin for detail check. His feedback was that the textures are matching the manual conversion.
I will make these converted paints available here in the download center after a few things have been cleared regarding approval etc.
I am also willing to do the same job for the whole set of C-130 textures. Batching or not... this will take some time. But the good news is that nobody has to do this manually.
Martin Wright is very generous man, and a great person to work with. His contribution has made this FSX conversion project really doable.