Yes, you have it right, The "Orphan" status means that the item is not used as a Featured Image, not inserted in the body of the post/page, and not actually displayed by any
[mla_gallery] shortcode. It's possible that the item is displayed by another plugin such as "NextGEN Gallery", but that's a problem I haven't addressed yet.
Sorting and filtering the list is done by adding appropriate SQL clauses to the database query that builds the list. The "where-used" processing cannot be done in this way. For example, to create the "Inserted in" entries every post/page in the database must be scanned to see if the file name(s) appear in the body of the post/page. For the "Gallery in" column, every [gallery] shortcode is found and executed to see which items are returned.
To minimize the processing load, this work is only done for the items displayed in the current page of the listing. To do the processing for all items, then sort the results would be much too processing intensive.
What I could do is provide a utility function that does the job only when asked for and then records the results as a category or tag or other taxonomy term, e.g., "orphan", "bad parent", "invalid parent". Then, you could filter the listing by those terms and do whatever you want with the results.
Would that be enough?