The commentary explains that ليس بعض primarily negates a universal affirmative, while «بعض ليس» directly states a particular negative. Treating their forms as identical can obscure the logical scope of negation.
Compare:
“Not every bird flies” — denial of universal affirmation.
“Some birds do not fly” — particular negative predication.
Under familiar logical assumptions their outcomes are closely connected, yet what is expressed directly differs. That is the central distinction discussed in the source notes.