How to make `adb reboot` work like `/system/bin/reboot`?
Write a script in your PC, look for 'reboot' argument, and execute your own command instead.

I do not know how a Window's compatible script would look like, but this is how a simple bash script would look like.


#!/bin/bash
ADB="PATH_TO_RENAMED_ADB_BINARY"

if [[ "$1" == "reboot" ]] && [[ -z ${2} ]]; then         # $1 is the first argument received by adb
    "$ADB" shell '/system/bin/reboot'    
else
    "$ADB" "$@"                            # $@ contains all the arguments received by adb
fi


Save the script as adb, give executable permission to it, rename adb binary with the name adb_orig, and then save this script as adb where adb is originally located.