The problem at play here is that Forestry's saplings are purely NBT-based, so setting a Custom Seed for them doesn't work that well. An example tree has this NBT data:

{
  IsAnalyzed: 0 as byte,
  Genome: {
    Chromosomes: [{
      UID1: "forestry.treePadauk",
      UID0: "forestry.treePadauk",
      Slot: 0 as byte
    }, {
      UID1: "forestry.heightLarge",
      UID0: "forestry.heightLarge",
      Slot: 1 as byte
    }, {
      UID1: "forestry.saplingsLower",
      UID0: "forestry.saplingsLower"
      Slot: 2 as byte
    }]
  }
}

Now, I know this is hell to support right, because this is one of these cases of pseudo-block-items which you essentially have to call right-click on the item itself to get it right, but it's an interesting case study for further block placing support.

This will have to be done in forestry's end.