> My understanding is that JPEGs don’t have lossless rotation by default, and that is true for sips as well.
This is incorrect. JPEG's can be losslessly rotated in 90 degree increments. See the -rotate option to 'jpegtran' in the libjpeg toolset.
https://man.archlinux.org/man/jpegtran.1.en
Best guess at what the author saw, the original files were likely originally compressed with an encoder that did not optimize the huffman table, and his newer tools likely do compute an optimal huffman table for compressing the DCT coefficients, that and the fact that the author was doing a lossy recompression would often result in file size reductions.
Also, passing jpeg's through jpegtran's lossless '-optimize' option often shrinks them in size. I.e., the jpeg's direct from most cameras often shrink (sometimes substantially) when optimizing them this way.