From:
Just-4-prawn
The Third girl appears the day after the house visit
Day 1: Yuu meets both Karin's & Confesses (Chp. 1&2)
Day 2: Yuu visits Karin's House & they start dating (Chp. 3)
Day 3: Shy Karin Appears (Chp. 4)
The shorts can't happen in the main timeline since there isn't time for the 3 to interact before Shy Karin appears. Thus the shorts aren't "canon" but an offshoot where Shy Karin didn't appear on Day 3.
Edit: Also the Karin's aren't individually named until after school on day 2 so the shorts can't happen until after Day 2. The Shorts also only refer to events that happen in the shorts (ie.
Short 3 refers to a page from
Short 1) and don't refer to the main story proper.