Can ffmpeg overlays be combined into a single output stream?
scale2ref consumes two inputs and then emits them both.. In your command, the output of the reference input isn't provided a label, nor connected elsewhere, nor fed to NULL output, so ffmpeg automatically maps it as output.

Use

ffmpeg -i LOGO.mp4 -i VIDEO.mp4 
       -filter_complex "[1][0]scale2ref=iw/2:-2[scaled][ref]; 
                        [ref][scaled]overlay=x=0:y=0[composite]" 
       -map [composite] 
       -y OUTPUT.mp4


The ref is now consumed by overlay and isn't left 'dangling' for ffmpeg to map.

As to your general query, just label the output of one overlay and feed it as the input to another, and you can combine them.