I dont know if this clarifies it but eto reply ng skillselect sakin:
βPlease note, there is no ability to amend the details in an EOI after a visa application has been lodged; however, the variation in your name between your EOI and visa application will not adversely impact your application.β
So if ilagay ung middle name or hindi should be fine. But for me just to be consistent sa mga documents ko, nilagay ko na lang ung middle name sa lodging. Hope this helps.