The problem there isn't the act of placing the biter bases - I could have the mod delete some trees and put them down, yes. The hard part it determining where they should be. Factorio's world is procedurally generated, and that's not just terrain but resources, enemies... trees.
This mod works by plugging into Factorio's procedural generation system and basically telling it there should be trees everywhere, but the type should vary according to the procedural system. It's still using Factorio's generation engine, just with some different parameters. This is also the problem with placing trees manually after generation, if I want it to look as nice as it currently does.
To manually place biter nests - or more accurately, to know where they should be placed - I'd basically have to write my own engine. To be honest, I don't have the first idea how to go about something that big.
If I do find some simple workaround I'll jump on that. When I have some time to spare, I'm planning to add a completely randomly tree placement mode as a workaround in the short term. It won't look as nice, but there will be biters in that mode at least.
