Alpha
So basically after a world generates, you're essentially left with image files and XML files.
Editing those image files directly can change biomes, roads, radiation and even the terrain.
Editing the xmls can change water heights and poi placement.
So what a lot of us do is run nitrogen to get a base map, then tweak as needed, i.e. what dam is talking about when he says "fallback features".
You had the right idea, editing the biomes.png, but it sounds like you did it in the wrong order. You want to do it after the world is generated not before.
About the only thing you can do before the world is generated is edit the height map itself, and use the import setting for that when generating a world. Then it will build a world around your height map.
The radiation map will scale with the world size, so if the border thickness is 10% of 512k then it will be 10% of 8192. So if it's 50 pixels in the small map it will be 800 in the large one.
If you want some ideas on how you can use nitrogen outside of just nitrogen, I have a few videos on my yt in an um, "Gaia" playlist. Might be worth checking out just to see the kind of potential that you can have.
touches on my workflow and this one expands on that