We now got a reply, and we have to say that we really appreciate the friendly and helpful attitude of the company regarding this issue. Here's what Sony Mobile's PR Manager had to say:
We are proud of providing the unlock feature to the developer community. Previously, there was a large risk of bricking the phone when unlocking with third party software. Sony Mobile’s solution remove’s that risk. When we initially provided the unlock feature, it was presumed that only highly skilled developers and super-users would take advantage of it. From blogs and discussion boards, it was clear that the community understood the risks and that unlocking largely voided the warranty. It appears that less sophisticated users (despite all our warnings) might be using the feature, and are now surprised by the consequences.
By the looks of it, Sony is more concerned with users flashing a custom ROM, rather than simply unlocking the bootloader. Still, the official also says that known issues (like the yellowish tint on the screen of the Xperia S), are OK and should be covered by your warranty, even if you've used the tool, yet, some customers complained that their warranty wasn't honored. We guess that it will simply depend on the repair center that you visit, or even the person that will examine your phone. At least, one thing is now certain - if you have unlocked your bootloader, you still have chances of getting repair service, but don't count too much on it.