So runes grant enough terrible power to level an entire city-state to ash in a single night...

As opposed to having them spread across the world so that when he needs to protect them he will always be too late.

He could either leave the nukes scattered all over the place where anyone who feels like they want a nuke today might stumble upon them, or he could find a way to seal them in what appears to be an incredibly secure vault, which only someone incredibly qualified who knows the sheer devastation they can unleash can access.

It's not a perfect solution but it trumps the alternative.

If runes are a sorce of magic then the petrified tree counters that and makes them weaker. The place was made to hold the runes so...

Better than building a golden glove and erasing half the univers tho. xD

It's a place that Ryze had to access with Realm Warp.

In a land full of trees that NULLIFY MAGICAL EFFECTS.

It's a damn secure vault.

'Course, Ryze may or may not know that absorbing magic in such quantities is what brough Galio to life...