If you scan in color/grayscale, it can’t use JBIG2 compression. The machine will likely use JPEG for lossy compression, could result in less crisp scans, but it eliminates this risk.
In my opinion, the only reasonable mode for JBIG2 is lossless, as the lossy mode of JBIG2 is, in general, prone to these character mangling issues. File sizes for lossless JBIG2 compression are already very low, so I would claim that using lossless is almost always worth it, unless character mangling is explicitly not a problem.