I'll look into adding some sorta effect descriptions for upgrades to both traders and the ingame menu, you're right it is a bit confusing right now, I guess I just didn't realize how confusing!
There is also a farming skill planned for the future (along with making it so resources don't respawn anymore), and idle upgrades to various mechanics like item processing. The incremental part of the game is a bit weak right now since I'm still figuring out core mechanics, but you can definitely expect to see that part get better in the future!
The factories plane is sparse by design for an upcoming mechanic, but I can imagine walking through a whole lot of nothing for a long period is probably not fun, I'll make a note on that and see if I can make it a bit more resource-dense or think of something else to improve on that.
Good catch on the apple tree, I can't believe I didn't think of that! I might have to rethink that card, but for the time being, you can restart/reload the game and the tree should respawn at the same place it was at before so you can still collect the card.
Thanks a lot for the feedback!