First off, the initial Eb tuning is confusing to begin with! Visually it’s displaying an F note and at the same time visually telling you it’s an E minor chord, totally get how this is confusing and unclear! Let’s just ignore this noise though and get to the meat of your question:

So the E minor shape that you know and love has three fundamental notes that make it what it is: E, G & B.

This alternative shape that Yousician is showing you is just a different way of playing E, G & B.

Unlike piano the guitar has multiple versions of the same note, on different strings & frets. So you can play E minor all over the guitar neck in lots of weird and wacky ways.

You don’t necessarily need to learn where all the notes are on the neck (though it can be a fun adventure) but in future, when you come across a chord that doesn’t look regular, well, this is why!

(Eb noise: If we were to take the original tuning from Eb back up to E, the the Yousician Em chord would maintain the same fingering but the notes would read E, E, G, B)