Copy audio stream, while also re-encoding with filters?
Use
ffmpeg -y -i in.mkv -map 0:v -map 0:a:0? -map 0:a:0? -map 0:a:1? -map 0:a:2? -map 0:a:3? -c copy -filter:a:1 "pan=stereo|FL=FC+0.25*FL+0.60*LFE|FR=FC+0.20*FR+0.60*LFE" -c:a:1 aac -b:a:1 192k -ac 2 out.mkv
-af is short for -filter:a which applies to all output audio streams. Add a stream number to qualify the application.