The only "correct" way I can think of is to have those two different heat shrinks be configurations within the same part file. Then in the BOM options you can tell it to treat different configs of the same part as the same item. However this will not work if you have other parts where you need the different configs to be treated as separate items (like hardware). In your situation I would probably do the manual cheat that you described.
I don't know what the brackets are.
I think I should just start my own shrink tube file with the different configs in it.
Configuration would be my way to do this, but, there is another way.
In one part file, on the "Configuration Properties > Bill of Material Options" box enter a User Specified Name the same as the your other part file.
In the drawing "Part Configuration Grouping" tab select "Display con......" this groups the same named parts on one BoM line with the correct quantity, the small one is saved as Part 1.sldprt and the large one as Part 2.sldprt with the BoM entry above.
Hope this helps.
I thought I tried that before posting the question, but I just tried it now, and it worked. No changes to the files because they already had the part numbers the same. I wonder if I can mark two responses as correct?
The parts in bracket are virtual components. They are not modelled parts but do exist in assembly for BOM purposes.
I have been long searching for combining similar parts with two different names. Being a big fan of Autodesk Inventor where it was very easy to perform such operation.