You're right, without the time limit, Shallie feels weird and unfocused. It also takes out the feeling that time is passing and it's like "I guess this whole game could have happened in a single week or something" so it takes out a certain feeling of growth you feel when you play an Atelier title.
If anything, the passage of the standard-ish 3 years cemented many Ateliers' narratives as stories about coming-of-age.
(Moreso in Arland than Dusk, though - Escha and Logy were pretty much the same at the start and end of the game)