Well I just spend half an hour typing and with a click on the wrong button I deleted my entire theory. My working days don't allow for a very deep explanation but i'll give the basic outlining.
Both realites are subrealities (normal, our universe, physical) part of a larger reality (paranormal, non physical, the mind, etc)
ALTtimeline is the original one, the unchanged one where Jacob didn interfere. It was not created by the incident or the planecrash.
The timeline they show us up untill season 5 is the altered one. This started in the time of the black rock. It started the moment Richard told Jacob he should infuence the outcome.
You can't understand the larger reality if bound to one subreality. Desmond can enter both realities and is conscious of it. Counsciousness (non physical) constitutes the larger reality. By acces to both realities Desmond might be able to understand the larger reality and become part of it. From this larger reality comes the ability to change the subsystems. My guess is that this is happening to Desmond right now.
This travelling between realities seems partially connected to desmonds contstant Penny and this constant makes it possible to reside in the larger reality, of consciousness. Without her it is not possible. maybe Jacobs indirect touch also might play a role.
I urge you to watch this link. And I might be blabbering but I can't bring myself to writing another full hour to explain it again, then accidentaly erase it again. But i will add to it if peope have questions as sone as I have the time.
https://www.youtube.com/watch?v=cCzkGsdQu2k&playnext_from=TL&videos=Xavb7L23bD4