I have been reading the product documentation for the new BOM tool.
Page Assemblies/Bill of Materials/Select Bill of Materials items
It talks at a bit about the functionality of selecting an item in the BOM dialogue and it highlighting the corresponding item in the component browser and vice versa. It indeed does not say anything further than this.
If I see a dialogue with the ability to select some of them, my assumption is that this action of selecting items is going to be reflected in the output. It is after all a selection tick box and that is the expected behavior.
As far as I can see the selection boxes in the BILL OF MATERIALS dialogue performs no function other than when you click on it it highlights the corresponding component in the browser.
I found the user interface metaphor of a selection box here confusing.
I currently use BOM Creator from the app store and it mostly has done what I have wanted. The main problem however is that my design will be using a model I have obtained from a vendor. A recent example is I have a model for a rack mount lithium battery pack. This model is made from literally a hundred components down to the last screw and washer it is composed from and I don't want them in my BOM, just one line item for the battery.
When I saw check boxes on the BOM dialog I thought great, I will be able to select the top level component but not all the irrelevant bits it is composed of. That would be top of my wish list for a BOM tool. A way to specify this component should be in the BOM but not its sub-components.