People enter and go out of companies all the time. If you're not Nintendo, of course. lol
Less so in Japan but it's becoming more frequent lately.
As for Baba it's two companies he left in a 2-3y span, the latest being one where he was the head of an external studio specifically created for a project that has yet to be released.
From the get go it was odd that he also wasn't at the forefront of the new company picture, might have been a sign.
If anything the first conclusion to draw (which might be wrong mind) is that something is wrong with Baba, he worked for 2y or so and delivered nothing.
Now if later on Prelude Rune is cancelled or we hear things about Square-Enix promising stuff to him that they didn't deliver (like budget or creative freedom) it would change the outlook, let's see if he's able to get hired somewhere else as well or not.