Does this really mean that several permanently-daily-scheduled jobs run after cron start, however system downtime causes missed schedules, and some missed jobs get in first?
was an earlier theory, however it’s not certain. So you’re sure yours is looking random?

Trigger the jobs via CLI: I like the GUI for defining the jobs and seeing the logs.
They are not mutually exclusive. Duplicati 2.0 could start GUI jobs from CLI using:
A command line client for controlling the Duplicati Server (third party contribution)
ServerUtil is for Duplicati 2.1, and has more in it than the documentation mentions:
Commands:
pause <duration> Pauses the server []
resume Resumes the server
list-backups List all backups
run <backup> Runs a backup
login Logs in to the server
change-password <new-password> Changes the server password
logout Logs out of the server
import <file> <passphrase> Import a backup configuration
export <backups> Export a backup configuration
health Checks the server health endpoint
issue-forever-token Issues a long-lived access token
status Gets the server status
One approach (if the “missed” run order is truly random – which maybe dev can resolve) would be to have cron start Duplicati as current, and either run the first backup or let it be permanently scheduled. First job has run-script-after to run the second, etc. Force chain.