A few mostly unimportant questions:

Is the NEURAL PROCESSOR LOGIC BOARD the last official challenge? The final email implies there may be more. Trying to answer the question myself, the answer appears to be "yes" based on the available descriptions and emails in the game data. I guess that apart from optimization, that means I completed the game.

Also, what is this "limited edition" and what might one find in the sealed envelope?

Also, has anyone benefited from using the programmable logic array (or any logic gates for that matter)? I used one logic gate (a '32) total in all my designs, so I'm guessing it's for prototyping only.

You probably know the answers to this already, but: Yes. Maybe there were plans to make more levels back then. Maybe there still are, though judging by how previous Zachtronics games went there probably won't be. From what I read, an "officia" invitation to Avalon city and a post card.
Back then the Avalon campaign wasn't available yet. It was added in an update later. (Based on the original campaign; haven't finished Avalon City yet).

Not really. I only used an AND logic gate once.
The array seems to be a huge saver for lines of code, but cost and power wise it seems wasteful.