Even though there are many people in Tokyo, it is well organized.
Darin always provides well-reasoned explanations.
The neatly arranged wine bottles on the shelves of the Tofugu office were all emptied out by Mami.
When you arrange things in the way that nature intended, you're doing things in a quite orderly fashion. This is the natural state of things, nice and arranged and natural. Orderly!
This is a jukugo word, which usually means on'yomi readings from the kanji. If you know the readings of your kanji you'll know how to read this as well.