Whether LEU is shipped in one go or in stages, Iran just cannot use it for making a bomb. Iran never planned to use this LEU to make a bomb anyways. Doing it in stages allows Iran to ensure compliance by the West. Otherwise what is to say that the West will not confiscate the LEU for good. The theory that Iran will "replace" LEU as it is shipped is nonsense, because if so then the treaty is useless even if LEU is shipped in one go. Because the entire LEU can be replaced in 18 months anyways. The only goal achievable by this treaty is "confidence building" and Iran's counter offer addresses it way more effectively than the original proposal.
Ofir Akunis officially replaces Danny Danon as minister of science, technology, and space (Haaretz)
from the article: U.S. awaiting formal response from Iran on nuclear draft deal