With the Bill of Materials, there is an underlining concept of level of details you want. Depending of whom is going to use the BOM, you need to adjust the zoom level. To each line in a BOM corresponds something that you need to get with one way or another. Buying it or manufacturing it yourself won’t be done with the same level of details. This is the concept of the Scope of Supply: the more you zoom, the more lines you have in your BOM, the more components you have to source yourself.
Several file formats can be imported into SolidWorks but some are more effective than others. When you have the choice between multiple formats, you should pick the best one: the one which contains the most information. One should not just simply import a model into SolidWorks, there are good importation practices to follow.
There is a feature in SolidWorks that is not particularly advertised but which is quite convenient when you don’t know what to do with certain components inside an assembly. It is the ability to make any component inside a parent assembly virtual.
To make a modification to a component, the most logical way is to add some features directly in it and make a drawing to describe the modifications. A note can be displayed to identify the source component. But in the Bill Of Materials, the unaltered component never appears which leads to a high risk of forgetting to acquire it in the first place.