Japanese students start their year in April. Pokemon is originally Japanese. Most VNs have the school year also start in April. The reason PAL starts in April is because it's logical a for it to be in April.
You have scored the first goal of the match. It's true that Kanto, Johto, Hoenn, and Sinnoh make (in great part) Japan, with Almia and some others....
So, know you make some things "light up", I have a new "theory" about the composition of a year in Kobukan Academy, I will use an argumentation:
-So the special region introduced in PAL is name "Kobukan", a name sound very japanese in fact.
-So you have surely right about the times of beginning the year in april... But if I reffer to the Assassination Classroom anime's, they have their summer holidays (about 2 months) in the middle of their year!
-So with this informations, this probably mean a school year will be about 9-10 months of school, 2 months of summer holidays, with probably some weeks of vacations before April...