Eventually you will reach a Zen state where you understand that the BOM is the BOM -- it is a map and not the territory. Like all maps, it reflects our best attempt to render our understanding of the territory at a specific point in time. The territory, like all territory, continues to change -- as it has before you drew the map, and as it will do after you have drawn the map.
Don't freak if it's not perfect. The ground will shift under your feet anyway by the time you get to put the plan in motion. Take pride in doing your best: adapt, improvise, overcome.