Yep, i’m pretty sure they programmed it that way on purpose just to make one of the powers you get later seem more useful.
… however after many hours in the game I started just using mod commands to make the wind go whatever direction I wanted, just like in Windwaker.
The Zelda team reached out to Monolith (Xenoblade team) for help with world building for BotW and TotK, Gamefreak needs to suck it up and do the same.