You need to configure the "Grouped Columns" options in the upper left hand corner of the BOM generation dialog box. Currently you have 1) Designator, 2) Footprint, then 3) Comment…. meaning it will first group objects by designator, then any objects with the same designator will then be sub-grouped into items that have the same footprint, and likewise with the comment as well. Since all designators on your assembly are unique (or should be), you are stuck with a single line item for each designator. That's clearly not what you want. You need to change the grouping options into something that will work for your parts and their parameters. Also be sure to check/uncheck the parameters that you want shown on the BOM. Only the grouped columns effect the grouping. The "All Columns" area just determines what additional parameters are shown and have no effect on grouping. You should just be able to drag and drop the various parameters between the "grouped" and "all" sections.
Do you have manufacturer's part numbers (or some company assigned PN) for the items on your board? If so, I would recommend grouping by that part number. If you have several components that are the same part (i.e a 10uF 0805 6.3V MLCC), I would expect that all of those components to share the same part number. And therefore if you only had "part number" listed in the grouping option, it would group all of the designators together that share that same part number. If you don't have a part number parameter, then I would probably group by value, footprint, comment, and maybe even description. You need to group by multiple parameters to ensure that the 1.0uF 0603s don't get grouped together with 0805 sized parts and you'll have to mess with the order that those are listed in to ensure they get grouped as desired.
In my case, I use our company assigned unique part number as my grouping designation. I usually also add footprint, and comment as well since it allows me to quickly identify any items that have potentially incorrect comments/footprints. If one of those items is incorrect on a particular part, i will see duplicate line items with the same part number.
That should work for you. Good luck.
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I just noticed that you have a few Digikey part numbers in your parameter list. If those are populated, then you could use that as your grouping parameter. The two 100uF caps as you pointed out in the original post should likely share the same Digikey PN.