Maybe they were charged by the component for installation? Or the packaged allowed for better placing & routing of signals?
RN3 is the 22 ohm resistors for the USB D+/D- lines. The 2 leftover would not really be usable, 22 ohm is not good for much in the digital world, its location between the USB connector the Atmega16U2 makes it awkward to route to & from, and you wouldn't want other signals to cause interference on the USB data lines.
One resistor network package vs two small resistor parts?
22 ohm are available in multiple sizes
https://www.digikey.com/en/products/filter/chip-resistor-surface-mount/52?s=N4IgjCBcpgbFoDGUBmBDANgZwKYBoQB7KAbRAGYBOABgHYAOEAqsAVkecoCYAWeAXQIAHAC5QQAZREAnAJYA7AOYgAvgS7V6rBCGSR02fEVIguXAAQB5ABYBbLCEEhR4gKrzZIyygCyONFgArtI4qgQAtFw6ejKBRsSQZNoElI7CYpAgqmqmJmbmhHaOKkA
As are Isolated resistor networks
https://www.digikey.com/en/products/filter/resistor-networks-arrays/50?s=N4IgjCBcodIMZQGYEMA2BnApgGhAeygG1wAWANgFZTKQBdPABwBcoQBlZgJwEsA7AOYgAvngCcUUIkipMuAsRABmcmEoAmCAxAs2nXoJF5yEuNNnY8hSCVIAGMUsf0mrSB278ho8GIAcplLI6JYKNiB2LjpuHgbeeOpKYKSSCMFyVorqdknkAOxRuu76XkYgALTqqdLcAK7y1iS04oUxZeWBaZB1DYparmwiwsJAA
Both seem to have a minimum price of $0.1, so two 22 ohms would be twice the price of one 4x22 ohm, and at the volumes these boards are made at that can add up to some savings.
RN4 is 1K current limit resistors for the Rx and Tx LEDs, and they have 2 in parallel for the 500 ohm equivalent the Green Power LED so it is brighter.
Pick N Place machine would not care, they can do 0201, 0402, 0603, 0805 parts readily enough.
I won't go smaller than 0805 for boards we hand place parts on. Others can handle smaller parts easier than we can. And if you drop one, forget it - one bounce and they disappear!