If I understand it correctly there will be multiple harem constellations, right? Depending on the constellation different characters prove to be harem members where others would be flings. If this is the case, then I'd say this an awesome way of implementing harem story-wise. This would do the interpersonal chemistry between female harem members some justice you rarely see in other games.
Only game with real good emphasis on chemistry between the female members I can currently think of is cozy cafe. The harem members "grow" into the harem, although they are always warned what is expected from them otherwise they can gtfo.
