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I think you would have to reduce the drop rate of saplings as well so it averages 1 per 10 trees or something or you could just go out for 20 mins and grind saplings from leaves fairly easily. So it might take a few in game days to grow but you could grow hundreds of trees fairly easily.

Eliminate the growth effect of bonemeal on trees. It would require more land to have a tree farm. When you plant a large tree farm you eliminate the need for bonemeal anyway. The probability of one sapling growing each second approaches 1.

Why not just keep track of all trees? If you destroy a tree, its carbon go back into the atmosphere. Just like normal trees; life doesn’t differentiate between planted or ‘natural’.