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Assuming you don't want to just paint vertex colors to remove them, you can add a points node (under the MASH utilities). Set it display point ID, then enter the ID numbers of the instances you want to hide into the visibility node.
So, back to my original kinda question -- is there some reason you cannot kill the trees around the edge by painting a strength map? The ID approach is obviously ID specific, so as you say if you change your instance count then the IDs of the problem trees are going to change.
I guess I'd also be interested in what situation it is you have where it's so important to have trees right to the very edge of the mesh, but not outside it 😉
Normally there are workarounds for this type of problem, so as having one non-rendering mesh for your MASH placement and another for rendering, or a transparency map on a mesh larger than your tree placement area, or post masking, or.... or.... It's often better to take the path of least resistance.
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