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

I’m pretty sure you have understood correctly

but - just because you have triggered a rule does not mean it’ll get to execute anything, waiting for resource at this busy time.

You don’t need the hacky file rename stuff; it’s not even going to work with UI entered rules anyway.

Which puts you back to a timer based solution.
One simple way, have a dummy Switch Item called EnableMessages or something. Make sure it is not included in persistence restore-on-startup, so it always starts as NULL state.
Give it an expire of whatever time you want, to state ON.
Have a startup rule update it to OFF (which starts timing)…
Grotty bit, amend your rules to only send messages when Item ON.