It is a limitation of the blueprint to save having to check potentially thousands of blocks above it given the range a terraformer will go in the x/z planes too. The blueprints in general are wide but quite flat in their range thus not especially suited to mountains. There's always the mining laser or mining drill if you need to clear one though 
It would probably be better just to do a blueprint that does primarily go vertically rather than horizontally, the Terraformer isn't especially complicated or configurable for needing a GUI. I've considered blueprints that actually change biomes too (rather than just blocks), so maybe a Terraformer expansion is due.
Good to see you managed to work out a solution, whilst not the fastest the advanced miner is probably one of the more power efficient options for mountain clearing.
