Amarula - yes I had considered aliens eat dirt/mineral matter. On earth creatures of this type (e.g. the lowly worm) are actually eating microbes. So Factorio worms could very well be eating 'dirt'.
The biters I see as the potential predatory types. The spitters as herbivores with cool defenses. Here on earth we've several species that spit acid!
Drakken - I hope that map generation rules are applied on top of a users preferred settings. So when you ask for maxed out biters and desert you get that. That shouldn't change at all. What would change is after your settings, the algorithm for ecological aspects of what you've asked for kicks in to paint it. There'd be a standard template of how these rules apply (default), and user settings can alter that to more/less of things in both density and frequency much like things are done now. The desert fluff on the ground would be more specific to deserts, edges would show changes in floral patterns not just randomly spray painted kind of thing.
These 'rules' for ecology could also lend weight to any potential future edition, where exploration of the planets resources might shift from mineral to mineral and biological entities. The potential is enormous. Then specific ecotypes are required for specific crops, habitat, etc...
Regardless, I think it might be relatively easy to implement? Categorise trees and widgets for specific ecotype/s. Set their frequencies so some are favored over others to mirror typical distribution patterns. Densities are up to the user, default densities to game creators. There's also rules about distribution. Basically even, clumped, and scattered random. Even is rare. More an anomaly. Entities could have differing distributions according to ecotype if they are shared across more than one, further allowing for individual looks/feels to specific situations.
There are three types of aliens (so far). Distribution might be (for default) more strategic. So they get distributed with a higher probability of being placed beside rocks or water, or in trees. So if x amount of biters was to cover y chunks of real estate, that still applies but they'd be more likely to be densest near the water and vegetation, or rock cover. Migrations likewise might settle in 'better' locations in that, when they migrate, if they encounter predetermined conditions after (and before) covering a certain distance, they settle on the spot.