There is a fundamental problem with the way biter bases spawn in vanilla. In short, reducing the frequency of biter bases makes a tiny difference in number of bases and an enormous (inverse) difference in their size. I hated the default way they spawn because it forces me to stomp biter bases constantly in order to explore new territory, as the bases are far too close together to slip past without being attacked even in the rare case that an optimal path is clear of rocks and trees. But the best alternative I can get is to set base frequency "Very Low" and base size "Very Small" which leads to vast swarms of biter base with narrow channels between them which are sometimes barely large enough to fit through without being attacked, and often do not give you a way through. In such a map, the biters occupy 15% or less of the total space, but there is as little as 5% usable space in the rare larger clearings, in which you have enough room to build a tiny base without getting instant turret aggro even before you begin making pollution.

I'm trying to keep this post short, but I played with the settings in RSO at some point and could not get a suitable compromise. It was easy to have biter bases spread very far apart, making long distance travel easy, even too easy. But what bases I did have were in very strange arrangements that looked very synthetic and unnatural. I like the shape of the vanilla biter bases especially when they get large, and I like the general structure of the landscape with very low/very small in that there are pathways between bases and clearings where you might find resources, but much of the land must be either taken by force or ignored.

My question is twofold:
1.) How do I make biter base generation more organic in appearance?
2.) How do I make the bases larger than one chunk, such that they aggregate in large colonies and completely control some of the land while still leaving some areas wide open?

I'm not really sure what do you mean by 1). And only way to change that in RSO is to change algorithm that rolls enemy bases.
Generating bases bigger then chunk should be possible already - especially with size set to very big. I might need to check that since there were few bugs there at some point.
General issue here is that in theory when current chunk is generated neighbouring ones might not exist yet. And going around this limitation is pretty difficult and would require pretty significant restructuring of spawning code.

Perhaps instead of overriding the perlin noise function, you could work with it and enable the mod to change the settings in ways that the vanilla game doesn't provide? The devs have failed to realize that in reducing base frequency, it increases base size by a far greater amount than changing the base size setting, and increases, rather than decreases, total amount of spawners. I believe it is because they are using a noise smoothing function which makes the peaks and troughs less jagged. What they appear to have forgotten is that smoothing the peaks can alter the ratio at x altitude, thus requiring testing to find a suitable x offset for a given smoothing change. (x altitude is directly altered by the biter base size setting, in which smaller bases increases altitude)

There is no good way to merge those approaches.
I'm still planning to use perlin noise for one reason but that will only improve quality of random generation in regions overall.
Perlin noise characteristics will always mean that frequency change does the same thing etc. And I still find the perlin noise controls pretty cryptic - working with them would require much better understanding of how it works. There are few Wiki articles and there was one FFF I think on the topic but it's still pretty tricky to understand fully.

It's really not clear for me what does it mean that layout is more organic. I will take a look at some bases created by base game and maybe figure out what you mean :D
I think that any significant changes to base generation would not take place before 0.17.

One way to push past difficulty with the function is to simply give players more control. If you let them adjust the settings directly and they don't understand them, just give them some default settings, or have a button that lets them use vanilla settings. And then if some players find a way to make good settings that don't exist in vanilla, they can tell you what settings they used, or maybe explain what's happening when they make a given change.

I don't understand Perlin noise by reading about it, but I'm gaining a seat-of-the-pants understanding by using it. I think if I were given control of the settings, I could figure out how it works, and I'd be able to explain how to tweak the settings to achieve a desired result.

I'm in no hurry here, I've been wrestling with this issue since I started playing in 0.12.

There is an option to disable RSO biter spawning and stay with base game one if you prefer. You can then play around with it in separate mod easily.

Yes I am aware of that. I'm posting here because I find both options to be so far sub-optimal that it's difficult to enjoy the game even with the best settings. I've been making posts about it in suggestions but it's getting ignored, so I came here to see if there was anything you could do to fix it.

Main question is: can you describe what would you find to be a nice base layout?
(And can we move this to forums?)