If the universe had a beginning (not eternal), then that gives a reason for thinking there is something that caused it to begin. That thing would be ‘outside’ the universe, so to speak. What would it be like for that thing (such as the Christian God) to be outside the universe, including outside time?
Since so many of our concepts and so much of our language is conditioned by or grows out of our experience of passing time, it is difficult to even talk about what it is like to not be in passing time. Perhaps, however, a useful analogy would be to viewing a series of tapestries. The tapestries in question, say, represent a procession of events through time. Say the Unicorn Tapestries, which illustrate the capturing of a unicorn.
To us, all the events are ‘happening’ simultaneously – we experience no procession of time from one event to the next, while looking at all simultaneously. Now consider interacting with the events. We can modify a given tapestry, yet we are not doing so inside the temporal events depicted in the tapestries.
When people talk about a non-natural cause affecting the universe, perhaps this is what the situation would be like, or would be a useful conceptual tool for thinking about the situation.