Well, I have some sort of personal theory for that, but still is pretty weak.
Maybe, and just maybe the gate it's made by Lucca.
You see, the planet, entity or whatever can create gates to relive it's memories and somehow try to improve them. Why, well... that's another topic.
The point in here is that maybe that gate it's different, because it doesn't relive a key-moment of the planet, it only change a point (a key point) in Lucca's life.
Obviously we can discuss the nature of the creator of the gate, but still it fuels from Lucca own memory.
Because of this, we can see two possible scenarios. (in fact there are a lot more, but I'll put the two great and more human ethical ones)
Good Scenario (A.K.A "The entity way"): In this possible solution, the gate it's fueled by the entity in an attempt to show Lucca an example of what it's doing. By helping his mom, probably Lucca gains a bit more understanding about the entity nature, early discussed, and why the gates and all the adventure took place.
This also leads to the fact that, besides what happens, the true power of fate it's ruled by intentions, free will and inner strengh... more than events, although these are obvioulsy important. (Such as what happens with the masamune after the ghost sidequest)
Bad Scenario (A.K.A "Lavos way"): In this possible solution, the gate it's fueled by Lavos in an attempt to stop Lucca from starting all the menace that the journey implies.
Still, things goes sour and besides the result, Lucca still become what she is... although her own motivation it's fueled by two different event... making probably a slight change, not in the events... but in her way to see the world.
The same fact it's re-stated in this explanation, inner strengh and free will are the true source of fate.
We can still think other way to see this event... and think that the entity itself created this gate, while all the other gates are created by the planet/Lavos struggle, in which the party it's a kind of inmunological system... or arbiter.
Maybe it's a gift, after all the long way and work Lucca has done. (Yeah, the party has seen and suffered a lot, but Lucca is probably the only one with the caliber to see the events behind that gate)
Of course this is just a silly theory... so there should be a lot flaw points.
Well, that's all.
Bye