I tried to fix our internal bitstream filtering on muxing using this code

https://github.com/FFmpeg/FFmpeg/blob/master/libavformat/tee.c

it works in sense it stopped crashing and adding simple filter like dump_extra makes file a bit bigger.

But complex stuff like cropping or rotation still does not work  :-(

not sure, may be we need to add those options via av_dict_set too ?