The answer to your first question is "No". You are better off creating a factory file. The parts list can be represented for each member of the factory iassembly.
Second question is if you go here "Tools" tab of your sub assembly change the setting as follows.
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Assuming that by "BOM" you mean a Parts List on a drawing (Bill of Material refers to something else in Inventor), there is a way (sort of), if the representation is a View Rep.
In your parts list, click Filter Settings. You'll be able to pick an Assembly View Representation as one of your possible filters, and it will only show parts that are visible in that View Representation.
However, it will not update quantities (there is a warning in the dialog box that explains this fact as well). If you have 20 bolts in an assembly, but only have 2 visible in the filter View Rep, the quantity will still show 20. It will only filter if all instances are being removed.
So, it depends on your situation whether this will work or not. If you are removing all of the like components in the View Rep, it could work. If you are only removing a portion of them, it will only make things more confusing. If you are doing a partial removal, you will probably need to use Cadmanto's suggestion of an iAssembly (factory).
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