Holy shit, the LN went crazy.
Lets go over what's different based on what i read, only 1 chapter behind.
Ozma and Illness are introduced early, we even get Illness backstory, which i am pretty sure didn't happen till the Afterstories in the WN.
Ozma was maneuvering secretly to help Kaito, though ultimately it didn't change anything in the grand scheme of things, but he along with Illness gave him advice to Kaito which helps him win over Kuro.
Contrasted to the WN, Shiro shows up when Kaito confronts Kuro and helps him, while Kaito mentally can handle Kuro in that he will never get scared of her, she also rejected him physically and obviously he doesn't have the power to oppose that, enter Shiro, again reiterated that Shiro and Kuro can null each other's power.
The LN kinda hints towards Shiro's true motives, while the WN it was vague until the final arc, interesting change, she helped Kaito cause she wanted to see what outcome he would bring, but him actually getting with Kuro has her feeling very complicated to say the least.
Now here is where shit hits the fan, the flashback to the war 20,000 years ago, proceeds the same as the WN, except we get more details on how the fights went, instead of being cut off.
Ein and Chronois are directly confirmed faster than light, also relooking at stuff i am kind of questioning an Infinite speed rating for them, basically distance is said to be irrelevant to them, as soon as they decide to go somewhere from a 3rd party's perspective, in less than a blink of an eye, Chronois is gone, she was there before, and the next gone, now is at the location she wanted to go to.
Isis can create an isolated space to trap her opponent, within which falls snow which gets pass the resistances of Gods like Life, touching said snow kills whatever it touches, ie kills your arm, kills your leg etc. Life dies, but comes back shortly after, as the concept of death doesn't exist for her, nobody can permanently kill Life except Shiro. Did i forget to mention Life actually got serious using her life abilities to boost herself, and shaking space itself with a step?
Fate is on some almighty type shit, when she gets serious and uses the eyes that see fate, she sees the past, present, future, we already knew this, but here is what we didn't know, once that's active her authority of fate is in affect, and fate which is her domain, extends to the whole entire world, does this mean world as in the planet of Trinia or the actual universe? Not specified so we would have to go with Trinia, regardless her ability would be on some planetary range.
Now here is the thing, within her domain no ability can be used without her permission, meaning once Fate gets serious, as long as you are in the world, you can't use none of your abilities.
Remember Fate's nature as a God is closest to Shiro and her golden eyes, the eyes which see fate are what Shiro naturally has, meaning it's pretty clear why Shiro has power null, no abilities can be used in her domain just like Fate.