Rule-Trigger "When the system has reached start level 40" not working to deactivate rules during openHAB startup

I doubt that. So long as something happened at startup, it would satisfy most users.

I thought I remembered seeing a github story where start level triggering was problematic, so as a stop-gap all rule triggers were treated as though 100, but I find no trace and likely confused something about old files syntax.

I do think your whole approach here is doomed though; you’ve no way (even with functional start levels) to ensure some particular rule runs before any other, to disable the others.
You need nothing to happen by default at startup, then actively enable messages later.