Currently it does not seem to be possible, using presets, to specify options to be inserted before the -i on the ffmpeg command line. Perhaps a new field could be added in the preset editor to allow this? I recently found myself needing to do this with a large number of files, and as far as I can tell, my only recourse was to create a wrapper script for ffmpeg which inserted the necessary options before the rest of the arguments.

For example, I needed the fflags option like this:

ffmpeg -fflags +genpts -i input.avi -codec copy output.mkv

Putting the fflags option after the input file doesn't work.