My method was to use simplified reps and create assembly level component parameters for the item balloon numbers. As they are part of the assembly, they work for all the simplified reps. Downside is that to create the balloons for any particular rep one has to create a matching repeat region. Upside is the balloon assignments can be done in advance of any drawing creation so that it can be added to / coordinated with an independent factory management software if desired (and at the assembly time) and not worry about having to "FIX" the order as the design changes. It also eliminates all problems with the repeat region reusing deleted items; one can create bulk items as place-holders for the removed ones if desired. Main complaint is that it's "tedious" to enter the same number for the cases of large qty's, but I figure a mapkey or other automation can be used if a huge problem exists in doing that.
Any items that have been missed will show up clumped together without an item number and any with the wrong number will likely duplicate a number from another item and should be as easy to spot as the usual repeat region errors from adding or deleting components.
Add the component parameter in a column of the family tree to see them; that can be exported to a file for any consistency review one might desire to to in Excel, for example.
And I emphasize - these are component parameters. They are not added in the individual parts. You can add an assembly component parameter column to the model tree and, when you click on the blank spot next to a component name, it will ask for the type and then ask for the value. Hence the value of a mapkey.
Much easier than layer management as every part of the way it works is visible.
From habit I always create a spreadsheet of sheet, view, and zone for all callouts. This makes it easy to ensure that no one has gone stupid and added multiple components directly on each other - a common feature when layers are used; people will have the wrong layers set, some component will be blanked, so they will figure it must have been deleted and then "fix" it by adding another copy, which will generally blend in perfectly with the original. It takes little of that to have extra screws and washers all over the place, showing as excess on the repeat region. To match that spreadsheet I create groups in the family tree of an installed component and the hardware that holds it in place. So, when I select a detail view I can also select the matching group and see what lights up.
Best of luck.