not sure if this has been suggested before.
but it is really difficult to find patches and i will admit i only just realized they need to stay patches to complete projects - it is tempting to plant a tree in the space and until a "newbie" comes across a project or a quest where they realize this, they will continue to plant trees in this space.
a quick solution would be to not be able to plant in certain ones or - as someone suggested somewhere else (sorry i forget who and where) maybe the seeds could not "take" in every place...
or the new trees could grow, be harvested once and then die on their own
just a thought