Bolt the Cat
Bringing the Thunder
In addition to what others have said, tectonic movement is on the scale of millions of years. It also doesn't account for the changing of landmasses the way you'd see it between Hisui and modern Sinnoh. The movement of tectonic plates causes landmasses to break apart (like South America and Africa), smash together forming mountains (India and the rest of Asia creating the Himalayas), or slide against each other (western California with the rest of North America).
Also remember that the Pokemon world has powerful legendary Pokemon that are capable of supernatural feats. So it's feasible that larger and quicker changes in landmass and tectonic plates could be caused by legendary Pokemon. In Hisui/Sinnoh's case, it could be due to spatial distortions caused by Palkia.