If both the screen and the phase-detection AF are out of focus, then it can't be the screen. So, Pentax would have no right to claim that the 3rd party screen could cause this. Plus, putting a screen in is not an unsanctioned hack either. But yes, I would not send in the camera with the KatzEye screen anyway, for the same reason I wouldn't include my SD Card or other non-essential parts.
JimmyDranox makes an interesting point. I do not agree with that, though, because if the secondary mirror would be out of line, then that would only affect the AF sensor but not the screen.
I just don't want to send in the camera right now if there's possibly an easy fix as I need it in 3 weeks and I have my doubts I'd get it back by then.
However, I have found a discussion thread, at dpreview, I believe, where someone quite familiar with Pentax repair manuals, claimed that it's rather normal that the mirror system ages and shifts over the years, and says that that's the reason why Pentax offers a tune-up and suggests to have the body serviced regularly (in 1-2 year intervals). He also explained that the body has active compensations depending on the temperature for that, too. The thread was about the K-10D, but I wonder if the same still applies, if it's true what he wrote.
I cannot find the thread again but I found this with a nice picture of showing the whole mirror + AF system in case someone here hasn't seen it yet:
Re: Badly aligned focus on K10D - tested!: Pentax SLR Talk Forum: Digital Photography Review
But at least I found the post I had in mind when I asked about making adjustments myself. See here:
RiceHigh's Pentax Blog: Hardware Adjust a Pentax DSLR for the AF
Still, I guess I'd need the K-3 service manual for that, and that's rather difficult to find.