Two sort orders are offered and the difference matters more than it sounds. Plain alphabetical order compares character by character, so item10 comes before item2 — "1" really does sort before "2" — and that is correct and almost never what was wanted from a list of filenames, versions or identifiers. Natural order compares runs of digits as numbers, so item2, item10 and v1.9.0 before v1.10.0 all come out the way a person would write them. Sorting by length is also available, with ties broken by content so the result is reproducible rather than dependent on the engine.
The operations run in a fixed order, because the order changes the answer: trim, then remove empty lines, then deduplicate, then sort, then reverse, then number. Trimming before deduplicating means "a" and "a " collapse into one line; the other way round leaves both, which is almost never intended when both boxes are ticked. Removing blanks before sorting stops them piling up at the top of the result.
Deduplication keeps the first spelling it encountered, so with case-insensitive matching on, "Apple" survives and "apple" is dropped rather than the text being normalised to one case. Input is split on CRLF, CR and LF alike, so a file written on Windows behaves the same as one written anywhere else, and the output is joined with plain newlines.