Yes, it'll take up more space on your atlas, which may cause you to need more atlas pages which increases the draw call count and eats up more VRAM.
Spine editor was recently updated so it's easy to trim/pre-strip your images after you've already defined the mesh. It used to be a problem, but this new feature fixed it. It was added in 2.0.23.
Just trim your images in photoshop or gimp and realign them in the editor so you won't need stripping.
