It is identical, because the CUE holds all track informations. He might be a bit confused about that, but what the hell I know. Apps like ImgBurn, Alcohol etc. make 1:1 copies of the scanned material, so the filesize of the combined BIN might be different (2 headers to 1 header etc.), but the game, the data, the audio, everything is a 1:1 copy. As if you would convert WAV to FLAC and then to back WAV and again to FLAC and last to WAV again. They always should be identical in audio quality or length etc., because they are both lossless. Combining two BINs is not like converting WAV to MP3 (which is lossy).
I made a bin/cue image of my Sonic CD I bought a while back, and you're saying that bin/cue isn't identical to the actual disc? How so?