Pokemon transferred in this way are modified in order to be legal in future games, though there are some quirks that mean they won't be considered legal until they arrive in a certain generation. You can find a table detailing this here. For those interested in how it works, the creator also put together a video discussing the development process and exactly what's happening behind the curtain.
The application has had beta releases since December of last year, and got its 1.0.0 release just last week. If you're interested in trying it for yourself, you can find the GitHub repo linked below.
Poke Transporter GB GitHub