I ran into a similar problem with railroad ties.
Made a blueprint that places ISM instances along a spline. Above a certain number of ties, the engine would give me the same warning.
I solved it by making the bp a mix of ISM and child actor components.
Now I have a BP that spawns actors that construct ISM instances.
So inastead of 1 actor with 100 ISM instances, I have 10 child actors with 10 ISM instances.
Works fine 
Another idea:
Put half of the trees in a new sub level.
As lighting is built per level, lightmass will definitely not putting that in the same lightmap.