I made the following User-Defined-Command 'Custom Commands' and assigned it as an alias named "bkp" so I can backup the config via the command line, repeatedly to the same file:
Backup MC Config:
MC.BackupConfig FILE="C:\Users\dell\Downloads\MultiCommander_ConfigBackup(latest).zip" ONLY_CONFIG
Change path to the backup save path you want the ZIP saved in, once you make the User-Defined-Command and assign it "bkp" or whatever you choose as the Alias, you can backup MC from the Command Bar just typing "bkp" and hitting enter (it'll backup silently.) Each time you execute the command it'll overwrite the same file without prompt. Hope it helps !