These calculations are very simple, it is pretending as though the rider's weight is is in the centre of mass of the bike. Yes there will be huge differences in how the brakinf will effect the rear end. This is a very simple model!

Basically yes, the torque created on the rear end can send feed back through the swing arm into the shock, it will either "squat" (compress into the trave) or "Jack" (Extend the travel) Both of these effects will partially lock the shock up in one way or another. However this isn't always a bad thing, some riders prefer this. Fabien Barrel rides a bike nptorious for having brake problems, however he has had a floating caliper put on his bike to increase the amount of Squat he gets.

Companies like Specialized are always going to be saying how much of aterrible thing it is, and how their bikes are totally neutral. This is a gross exaggeration, it can be good for the rider and the horst link hasn't totally eliminated the "problem"