Modifiers mucking other modifiers sounds correct. Happens in Max as well. When you're satisfied with a modifier you might want to apply it so it's not a factor to cause issues later. Booleans are bad in every 3D program I've used. I would even suggest cheating more by not combining geometry if you don't need to. This will save time in repairing problems caused by boolean operations, and if you need to go back and modify the original geometry you can. Shapeways correctly calculates volume/pricing for intersecting geometry so you don't have to worry about that.