They hold “system binaries” meant for root user. It’s not a hard distinction but many if not most Linux fundamentals have their roots in very early computing, mainframes, Bell and Xerox, and this good idea has been carried into the here&now. Not sure about the provenance of this one, but it makes sense. isn’t /mnt /media different between distros? These aren’t hard and fast rules - some distros choose to keep files elsewhere from the “standard”.
/bin and /usr/bin, one is typically a symbolic link to another - they used to be stored on disks of different size, cost, and speed.