I, too, believe Thought's "Theme Theory" to be the most probable explanation as to how the time line operates. I have a variant view as to how it is changed, however.
As there was a clear agenda behind the events of Chrono Trigger, those of the -Entity-, it can be safely said that the eight chosen points in the time line were specified for a reason.
Crono and many of the other characters within the game are all Chrono Triggers. It was stated in Chrono Cross that by releasing strong enough feelings or desires one can change time.
Within these eight time periods, Crono and his friends found the desire to change the time line and then the power to do so.
Here is how I believe it works.
A Chrono Trigger who goes back in time and changes history does so out of desire to do so. This asserts a governing principle behind "what will happen next."
Each time traveler is still relative to their own place in time, so changes made would reflect upon that. Of all possibilities resultant from a change in the time line, the option closest to the desire of the Chrono Trigger is accepted into the time line.
This fairly well defines what "Chrono Trigger" means. It is an initiation of events in time.
Please accept this as less of a scientific concept, and more something fitting within Thought's "Theme Is Supreme"...because it is.
I stated here
http://www.chronocompendium.com/Forums/index.php/topic,5571.msg181204.html#new that I believe that the Frozen Flame is a device with which Lavos alters potential events in time to best provide for its slumbering physical body. So I state that the original time line before Crono passed first into AD 600 was one engineered to provide for the sleeping Lavos. It was a time line where the Frozen Flame introduced changes to the original species to insure their proliferation and evolution so that Lavos could collect their DNA.
Arbiters of the Flame are people who are literally the thrall of Lavos through the Frozen Flame. The Queen of Zeal did not build the Undersea Palace and Mammon Machine to empower Zeal...she did it because the Frozen Flame found humanity to be stagnating and in need of a "reboot." The Black Omen was a tall hill from which the Arbiter could closely watch over the time line like a shepherd over sheep.
All of history was manipulated away from extinction or stagnation until Lavos was ready.
The -Entity- chose eight specific eras to combat Lavos, and it chose certain people within those eras, all Chrono Triggers, to guide the time line back to one where Lavos is not present.
There is no way for me to ascertain if whether Crono and his friends were empowered as Chrono Triggers, or they just always were. The end of Chrono Trigger, with the Fall of Guardia, may suggest the former. Maybe without the -Entity- letting them Will the future, they got caught with their pants down?
One point where the time line changes quite drastically is the Undersea Palace scene.
In it there is a conflict between the Chrono Trigger and the Frozen Flame.
"The Chrono Trigger, if combined with the Frozen Flame, can (according to legend) grant unimaginable powers over time and space to the point that history can be shaped according to the will of the user of these two powers."
I believe that when Crono and party interrupted the ritual for Schala to activate the Mammon Machine, every person assembled was sent somewhere best suited to their unconscious desires. Though they knew not the destination, their subconscious need to fulfill certain goals figured that out for them.
I am getting pretty sleepy, so I will state that this is my feeling on the way time can be changed, though it is far from complete.
The very nature of the Chrono Trigger touches on the concept of 'reality is perception.'
I think with the right discussion this could be properly fleshed out. The game does evidence much of what I've said, just in subtle ways.
So?