Other than castings - I have never used base parts. This is how I deal with the issue using configurations.
Create the purchased part (default configuration). Add configuration properties Item_Code & Item_Description. Populate these properties with your purchasing information (you can add other properties as needed).
Create another configuration with modification (ie Modified). Populate the Item_Code & Item Desciption exactly as the purchased part.
Go to your excel template. Add two columns called Item_Code & Item_Description. Change the name of the cell (i.e. if you added Item_code as new column "D" then cell D1 needs to be name Item_Code) Note - the custom property and cell name must be identical to work.
This will also work with an assembly.
When you create a new drawing (of the modified part/assembly) - generating a new BOM will populate the item_code & description of the purchased part. Even though the drawing number, file name, etc.. are pointing to the modified part properties.
This same process allows me to deal with left and right hand versions of assemblies (such as wiring harnesses). The geometry may change for assembly purposes (i.e bend cable to left, right, up down, etc.... on installation). But the ordering information is identical. Thus, each configuration has the same Item_Code, and purchasing buys the correct number of assemblies. The work instructions (drawings) show representative geometry (bend instructions).
Best of both worlds.
Note - I've replied to this post in a hurry as I am at a client's site. Contact me via email if you need further explaination.
A Base part is really only another form of inputting geometry into a new part that can be parametrically linked to other parts built on the same model. This is ideal for a situation where you want all parts to be linked by common geometry.
The two options for you are: -
If you are to buy a part with it's own part number and then modify that part and give it a new number. Insert that part into an assembly as suggested by Kenneth, in this thread and give that the new number. This will result in the BOM being as you want it.
If you want a new part based on a previous design, you would want the geometry but not the part. In this case, you insert a base part, which as you have discovered does not appear in a BOM.
I believe SWX covers your needs already, as per the assembly model above. If they were to include the Base part in the BOM, I think it would cause bigger headaches for those of use that use Base Parts already.