2. AI aircraft is taking off from A>KE and not from A>Z onto RWY 31L as all aircraft would normally do in real life. Works perfect for 13R at PF
Test it and let me know please. I'd like to know if this is bug in the AFCAD
The AFCAD is surely correct. In fact, at least from a formal point of view, I'd say 31L looks even more correct than 13L, see the following screenshot:

First, the Glideslope is in its real world position, parallel to the touch down zone markings, and it's a standard 3.0 deg path. Localizer is located at the opposite end of the runway, as usual so, everything related to the ILS is surely correct in the AFCAD.
About AI, you can see the displaced threshold area is drawn in green in ADE, which means is not part of the runway, and this is precisely to prevent AI to land on the displaced threshold.
However, if you wanted to have AI taking off from the displaced threshold, coming from taxi Z, this would conflict with the above so, if we set the whole runway as a black ( runway ) link, AI would depart from Z, but they might also land there.