I have a theory of my own to present to you all. Hopefully this theory is widely accepted and I get my name passed on for generations as the guy who first thought of it...j/k
Anyway, my theory is called the Base Timeline Theory. All dimensions (timelines, for the sake of this argument) have one timeline that can be changed. When things change earlier on in the timeline, the later part of the timeline is discarded to the DBT and replaced with a newborn timeline. The fact that these events can happen and change these timelines, that timelines can interact with each other (Lavos pulling Chronopolis, the planet pulling Dinopolis, etc) shows that there was a time where those events hadn't happened. There was a time where the Entity didn't allow gates to open and make way for Crono and crew to change time. There was a time when Serge hadn't saved Schala and the dimension was split and connected closely and continued on its own path. Then came the time after the Chrono games happened and the Ideal timeline was born.
What am I saying? There is a specifically different "time" for all these events, one happened before the other progressively. My point is: there is a Base Timeline that all other timelines lie upon. While all other timelines have a beginning and end (The End of Time), this one doesn't, it has always existed and will always exist. The Base Timeline isn't necesarily the same world as the world of the Chronos, it's just a clock ticking time, essentially. The Darkness Beyond Time exists here, but is kept under some sort of watch by the one other 'thing' (for lack of more descriptive term) that resides here: the Entity. It can see all timelines in their entirety, from beginning to end. It can see all changes being made, watches as new timelines are born and old ones are discarded into the DBT.
The Entity decides it doesn't like the path the Lavos timeline is going and wants to change it, making it so the gates appear, watches all the changes occur all the way through the end of CC.