No, as I stated before in my email, changing the whole frame alpha value is not useful in my case.
Anyway I managed to find the solution myself: the "alpha" plugin works and provides a chroma-key feature that is exacly what I needed.
Now I have another problem: PgmImageSink (in pigment library) refuses to receive a stream with Alpha channel in it.
filesrc -> decodebin -> alpha -> pgmimagesink (doesn't work)
If I put an ffmpegcolorspace, the pipeline runs successfully but the alpha channel is filtered.
filesrc -> decodebin -> alpha -> ffmpegcolorspace -> pgmimagesink
Even using capsfilter to force a colorspace with alpha channel won't work.