I haven't played Harbour Town, but I do have a certain affinity for it as a spectator partly because it seems genuinely unique.
To me, the whole premise of this thread is flawed. The questions in the OP essentially ask "Why isn't it a bad thing that Harbour Town doesn't conform to all the hard-and-fast rules of good design?" My answer is that those hard-and-fast rules aren't hard-and-fast at all, and Harbour Town is special precisely because of the fact that it was conceived 50 years ago with the goal of breaking every trend in architecture at the time (to paraphrase Pete Dye's writing on it), and 5 decades later it's still a genuinely unique course that continues to push back against not only trends from when it was designed, but also trends since.
The questions in the OP can be categorized into three groups (with some that could be placed in multiple groups): (1) Questions insinuating poor conditioning that on-the-ground accounts confirm is no longer an issue on the property; (2) Questions that can be asked about lots of great courses where, for instance, the property might be fairly flat or have a tree or two in play in fairways or where a ball might bounce on a cart path once in a while; (3) Questions asking why Harbour Town doesn't need to conform to "the rules."
Group 1 is based on flawed assumptions to begin with, Group 2 is neither here nor there, and Group 3 is more revealing of the groupthink some of us rely on to avoid having to do the hard work of analyzing courses that break the mold than it is revealing of any shortcomings with Harbour Town.
There's another thread right now where RonMon is trying to come up with a list of courses that pose a challenge similar to Harbour Town. I think he has three courses on the list last I checked, and the third was a stretch. It's not surprising that a truly unique course would be polarizing and hard to categorize and appreciate with the same criteria we apply to courses that fit more neatly into the box. What's amazing is that Harbour Town has spent 50 years outside the box.