Hi, love the idea of custom trees and our server would love it but the loss of normal vanilla trees is a concern. Maybe there is already an option to it but I would suggest to have a alternative triggers. Here are some that I just made up on the fly.

• check for nametag on used items
  Could be either to name the saplings to something specific, though I don't know if saplings lose that data when placed or to generate custom trees one could use named bonemeal e.g 'fertilizer'

• use another item to fertilize instead of bonemeal

• check for player sneaking whilst bonemealing