Thanks zft for clarifying - you make some good points. That being said, all of the Intermediate "split" programs that I saw in the gray book (SS:PP) do actually have squat + press (or squat + bench) workouts listed on the same day, and the squat is always listed first (the only exception I can think of is the "1 workout a day" split, which obviously has all lifts on separate days). This is why I'm thinking there must be a good reason for it.
For technique-sensitive Olympic lifts (snatch, clean, jerk, etc.), I totally agree that the squat should be done AFTER these lifts, for the reasons you mentioned. But I don't think the OHP is nearly as technique-sensitive as the Olympic lifts; plus it doesn't involve as much lower body as the Olympic lifts (or the squat), which may be why it's okay to OHP after squatting.
Either way, perhaps it's time for me to try pressing before squatting again, to see how I do!