I initially expected 'appstore' to be アップストア
I don't see why it's translated as 'apuri-store'
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From what I can tell it's actually called the "App Store" in English letters, where they sell アプリ.
As for the reason they prefer アプリ...
Japanese like to shorten foreign borrowed words if they are longer than 3 or 4 sounds because unlike English, there is no good way to blend nicely like in English...you have to clearly say each.
Saying most foreign-derived words out in this long form becomes very cumbersome.
Another example would be バイト (ba-ee-to) shortened from アルバイト (ah-ru-ba-ee-toe) meaning part-time work which is derived from the German word "Arbeit" meaning work or job.
The word "application" in Japanese is
アプリケーションソフトウェア or just アプリケーション
which you would say ah-pu-ri-ke(long)-shon
The abbreviated version アプリ has been around a lot longer than the the word "app" has been used in English, probably since the first commercial software began to be sold in Japan in the 70's. Most commonly refering to desktop software or business software.
When the word "app" became popular after smartphones arrived, the Japanese already beat English to the "let's make that darn word shorter and cooler" punch... :)
They also use アプー (ap-pu) as well, to refer to just mobile apps. However the app store has both Apple desktop and mobile software...so I guess since アプリー is already so close to アプー there's no use in renaming all forms of software to newer "app".
That's my best guess....
There could also be some copyright reasons that I 'm not aware of!