When possible, use the filtered list to set and get checked list items.

Currently, if you:

1. Open a filter popup on an unfiltered list (i.e. the "All" checkbox is selected).
2. Search for a substring in the list.
3. Press "Apply"

All items that are selected, including items that are not visible due to the search, are applied to the column filter. This is not intuitive since you would only expect the items that matched the search in the popup to be applied. This change makes the application of the checked items only apply to those that match the search criteria.