There is no size difference between *.flv and *.mp4. The same recording, saved as *.flv instead of *.mp4 with the same compression settings, would have the same size. It would only differ in a few bytes or kilobytes. If videos are different in size, it's not the container but the video content that matters, or the compression settings.
You can shrink your videos by reducing the bitrate or using lower quality settings with your editing software, but this is not dependent on the container.