Your first request could be a problem. I use so-called "effect" on capsules, put it simply I tell Factorio "place entity [ID] in a place where thrown capsule landed" on an item prototype level and do nothing else leaving all job to be done by game engine. That's why we have 9 capsules in total, because vanilla Factorio has 9 trees species with their fixed ID (tree-1, tree-2, etc.) Unifying capsule into one would require me to write complex logic like "watching" where capsule landed and then pick random tree number and place it manually through runtime script, which I to be honest do not want to dive deep into.
About robots: I'm not sure if I understood correctly. I just checked, capsule-spawned trees could be deconstructed by robots perfectly fine when you use deconstruction plan on them. Or is it a request? You want bots to "watch" for dead trees and dismantle them automatically placing new tree on old place? Well, that's even greater scripting work than your first request.