Yeah there's no issue there, most codecs support variable bitrates and variable iframe-pacing, and ffmpeg will happily concat such files. Also, there's no need

Yeah there's no issue there, most codecs support variable bitrates and variable iframe-pacing, and ffmpeg will happily concat such files. Also, there's no need to render into an "uncompressed format" the i-frames are still compressed, and even in the naive case you'd only need small number of i-frames because you only need to replace any orphans in the cut GOP after which you can just go back to normal decoding.