I certainly agree with you that the Baron had a good grip on reality (not equally good in all places, but still a very effective leader). Still, I wouldn't make too much of the Harkonnen victory... are you trying to say it indicated an advantage over the Atreides way of thinking? I'd argue against that.

I would want to be clear about this: the Atreides may have a net advantage over the Harkonnen, but they are not 'strictly superior' to the Harkonnen in every respect. As the Baron explains in the full passage, the Atreides wagered on a strategy ('rabbits') that failed against the enemies they knew were gunning for them ('bees'), so at the very least, their planning was not so hot.

And they did have a plan based on a better understanding of at least some aspects of the situation: they understood the value of the Fremen, whom the Baron refused to acknowledge as important until Hawat opened his eyes.

Aspects which didn't matter until much later if you count Paul's resurgence, and which resurgence involved some pretty exotic factors I can't really blame the Harkonnens for missing.

One wonders what Piter bad been doing during the earlier Harkonnen reign

Being trained, perhaps. Remember that the Baron's twisted mentats were periodically killed off. The Terrible Duo aside, I don't think we know how long Piter was at the job - it is entirely possible he had been kept completely busy calculating out the loss of Arrakis and the subsequent invasion. Certainly Hawat (Piter's non-twisted counterpart) was kept full occupied by his counter-plotting.