Yeah, the game is really vague on what caused the dimensions to "split," which makes the "why" and "how" very difficult to determine. We aren't sure on the relationship between Home and Another, so the RD and Dragonian dimensions are even more troublesome to pin down.
BROJ and I discussed a while ago (as in probably over a year ago) the two possible "shapes" that the dimensions might take.
There is a Y shaped dimensional split (or Y-Split), in which at the point of the 50/50 chance Belthasar cites as when the flow of time split the dimensions are separate, but before that they are the same. Essentially, the dimensions only exist in the "future" from the perspective of the time point when the split happened.
This is sometimes also referred to as "Armageddon Branch" because when Crono & Co traveled from 12,000 BC to 1999 AD to kill Lavos, they would only travel to one dimension (and thus only save one dimension).
That is, there is no Home World or Another World in 1001 AD. So a change in the timeline then would affect both Home and Another.
Or there could be an H shaped dimensional split (or H-Split). When the 50/50 chance Belthasar mentioned occurred, both the "future" and the "past" were split. If one changed time, after the split occurred, in 1001 AD, it would only affect one dimension
Unfortunately, there isn't quite enough information to decide which split is the reality.
It was pointed out in another thread that Miguel remembers being in the "Sea" for 14 years. For 4 of those years, the sea was the Sea of Eden (and thus, he was in Chronopolis). But for 10 of those years, the sea was the Dead Sea (and thus, he was in the Tower of Gedon). That he remembers ever coming to the Sea of Eden implies a Y-Split; if it was an H-Split, then he should have only remembered the Dead Sea (as the Dead Sea would have always existed in Home World under an H split, but in a Y split those first 4 years would have been in the only dimensions). But such a theory doesn't take everything into consideration.
Doubly unfortunately, there isn't quite enough information to say exactly when the dimensional split occurred either. Consider this statement from Chronopolis:
Two worlds that are so close,
and yet so far in nature, exist
in different dimensions.
Under the surveillance of the
main computer of Chronopolis...
'"FATE."'
In other words, FATE, has
always been observing the 2
parallel worlds, and guiding them.
FATE has been manipulating the
world of El Nido, in order to
avoid any major change to the
history it knows.
If an event on El Nido
influences the main continent,
the year 2400, in which FATE
exists, would change.
This paradox could potentially
lead to great disaster...
The Records of Fate - FATE's Terminals -
collect data from around the world,
and input guidance directly into the
minds of its users.
In this discreet way, FATE is able
to control the lives of people
without them knowing.
Guided by fate, the people of
El Nido lead a harmonious life.
In a sense, they are nothing
more than puppets of FATE.
An instruction to the young girl
in Arni 01 to give up going to
the main continent as a poet.
An instruction to the man in
Arni 02 to give up becoming
a fisherman.
A plan to avoid any point of
contact with the main continent,
so as not to affect history.
However...
Ever since the formation of
the Dead Sea 10 years ago...
FATE has been unable to intervene
directly with World 01.
The best FATE could do was cross
the dimension and receive data
through the Records of Fate.
And with much difficulty, FATE
succeeded in binding Miguel
to the Dead Sea as a watchman...
This implies that there were split dimensions
before 1010. This split might have actually been in 2400AD, per Kid:
In the year 2400, during a
counter-time experiment, the
Flame goes out of control...
This causes the dimensions
to rip apart, resultin' in
the Time Crash.
Emphasis added. However, such an approach doesn't address the significance of Opassa beach; it is clearly established as a point of weakness between the two dimensions where a crossing is possible.
To note, however, such a crossing is also possible in the Dead Sea/Sea of Eden (but one can't access the DBT from that point, potentially indicating that the two distortions are of different varieties, or that the Game Programmers were lazy).
The best I have ever been able to come up with is that there are two types of dimensions:
Fundamental Dimensions and Secondary Dimensions.
Fundamental Dimensions would have been realities that have existed apart from every other "Fundamental Dimension" since the beginning of time. They represent different starting positions of the universe. Maybe Pi is a decimal point different in one dimension, gravity is slightly weaker in another, etc. Basic fundamental differences in the way the universe works which lead to different outcomes.
Secondary Dimensions are when Fundamental Dimension "split." The RD and Dragonian Dimensions seem to be Fundamental Dimensions while Home and Another seem to be Secondary Dimensions.
However, the actual proof for such a perspective is lacking, in game.