Moozzi applies filters designed to remove imperfections in the source, then encodes with high quality settings. The audio is usually lossless from the BD and commentary tracks are included. He's easily the best encoder out there. The only thing I've ever seen him do wrong was transcode the audio from the Marmalade Boy BDs to AAC. If he ever does another one with FLAC audio he'll be perfect in my book.
The difference is much bigger on older titles from the cel era. The BDs tend to be sloppy noisy messes that were thrown together as cheaply as possible with no attention to quality. The work he did on Dirty Pair (for example) completely redeemed the BDs and is a vastly superior product when compared to the original.
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