I know it's been discussed before in other posts, but I still don't have a workable understanding of how it is decided, which is only a secondary problem right now.

The primary issue is twofold.

1) Per the rules, it doesn't change.

2) Per the Core book, a dragon's Natura/Gnosis changes depending on their age/level.

I can't reconcile the two. Is there any way to explain this so that the rules make sense? or are at least uniform across the world.

You are going to be sorely disappointed if you're hoping for perfect consistency in Anima. The larger the rule is (as in the more widespread) the more exceptions it tends to have in Anima. That being said, this situation isn't quite as contradictory as you might think.

First off, having been over the Gnosis and Natura sections many times I can say with confidence that the confusion comes from the following passage in Gaia 1.

When the Game Master begins a campaign he must grant Gnosis as considered appropriate to each character depending on what plans he has in store for them. This value is unique and will NEVER change throughout their existence ; it is the important fate that they have from the moment they are born. Of course, the Game Master must be honest. If he had certain expectations at the beginning of the campaign, but this later opens up to new possibilities for game play, he is not obligated in any way to keep the Gnosis value he saw fit to bestow the characters at the start. He may simply increase or decrease it to his liking. He must only consider that it has always been its true value from the beginning. Typically, the Natura recommended for player characters is 10 (pg 295).

Correct me if I'm wrong, of course, but the core book never mentions Gnosis being unchanging, it's only here in the Natura section that we find this contradictory information. The problem here is either bad writing, or bad translation, though I'd blame the first more than the second in this case (I don't have the Spanish Gaia 1, so I can't say for certain). You see, in this passage (indeed, on the whole friggin' page), the words Gnosis and Natura are often used interchangeably, as though Gnosis was Natura, and Natura was Gnosis, despite the phrasing that separates the two. There's a reason (at least for the Anima creators) that the two aren't just one score.

In short: This section is meant to read that Natura never changes. Gnosis is seen to change in Ebudan, Dragons, anyone who has Chimera cast on them, anyone who uses Lordship over Nightmares/Dreams, and a host of other situations. Gnosis is malleable, and the more powerful a being becomes the more likely it is for its Gnosis to rise. In fact, the phrasing from the Core book is "Normally, a GM gives each character an initial Gnosis Score of 10" (Core 276). So, yeah, Gnosis changes, Natura doesn't. You can get more powerful, but you can never be more important than the universe deigned you to be from birth.

Hope this helps.