Yes as you said, Yoshiyuki from Da Capo II learned it from Junichi from Da Capo I. The protagonist from Da Capo III was the original creator of the Wagashi Creating spell since the main story takes place far in the past before Da Capo I even. Kiyotaka and Ricca Yoshino were the grandparents of Sakura and Junichi of the original Da Capo VN, were the ones who originally planted that Everlasting Sakura Tree that grants wishes, and Ricca aka Granny Yoshino taught Kiyotaka's spell to create Wagashi to Junichi. So, in all honesty Da Capo III sets the stage for Da Capo I in a very big way.