These are proprietary Windows tools that handle the heavy lifting. They have internal databases that recognize the structure of specific copy-protection schemes (like LaserLock or SecuROM) and attempt to unwrap them during the BIN-to-ISO conversion.
While many retro gaming emulators (like those for PS1 or PS2) support BIN/CUE, some modern front-ends or specific virtual hardware configurations require the standard ISO format for better stability. bin to iso converter