They're sticking to lossless optimizations, so they're only benefiting from the "jpegcrush" part of mozjpeg that chooses separation of progressive scans for best compression.
The difference would be bigger if they used mozjpeg for lossy (re)compression as well, as then they'd also get trellis quantization.
I don't think that fact that you're only looking at lossless compression is clear enough in the post. People see "JPEG" and "compression" and they assume you're talking about lossy compression. The post doesn't include the word "lossless" to describe what you're doing, people have to figure it out.
Happy to hear you're seeing benefits from mozjpeg, and I look forward to the results of your work optimizing run-time performance. Thanks for giving mozjpeg a shot, publishing your results, and contributing back!
The difference would be bigger if they used mozjpeg for lossy (re)compression as well, as then they'd also get trellis quantization.