I would like to know what is the suggested best method to apply a filter to a small part (in the meaning of X-Y dimension, not temporal) of the video.
In other words: how/is it possible to to select a only portion of the video where to apply the filter ?
It is definitely possible.
You can cut part of screen (the rest will be simply transparent), apply filter to this part and then put this modified version over original screen.
Try cookie cutter, chromakey. If it doesn't fit good enough you can paint/generate mask with black for transparent and white for solid color. Then put mask on new track over your filtered copy, set up track mixing mode as multiply and probably set track dependance.