Disable update check on Computer level
Most companies have users without administrative rights and if Draw.io prompts for an available update, it will create tickets to service desk. The timing to include the flag in the config file is hard, the user probably starts the app before IT can deploy it.
I would suggest having a central config file that overrides the user settings, or a config file that is inherited on first launch.
While not exactly the most elegant solution, I found that you can set a global environment variable to disable the update check:
setx /M DRAWIO_DISABLE_UPDATE true
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Maybe better, try to determine if user is admin on the computer and disable update for installable versions. https://stackoverflow.com/questions/3600322/check-if-the-current-user-is-administrator