Yes, I suppose mod compatibility is something I should perhaps keep in mind more myself, beyond just tree byproducts.
For one I do intend to do at least some building recipe changes depending on mods. Right now all I have in mind is Lumber and Wooden Gears from Wooden Industry, but there are likely more that would be appropriate.
Also I do know that Lumberyard would not work that well with tree planting or something like Noxys Trees. Just didn't occur to me at all when rewriting. My current logic will remove a lumberyard from the an internal list when all trees in range are destroyed - basically "turning them off" - but there is no logic to turn them back on if more trees appear. You'd have to pick up and replace the building. Maybe the logic in your mod is similar?
Space Age compatibility is something I expect you will be far ahead of me on. I didn't like SA, so I don't play or test in it. If any of my mods happen to work with it, great! But if not someone would have to provide me working code. That will limit the potential audience for my mods, but I'm okay with that.
I do like your idea of a Rock Harvester. The idea had occurred to me, but I hadn't even thought to start putting it in to action.