It's hard to answer based on this example.

Imagine the gate agent has called Zone 1 and Zone 2
who are almost finished processing. You, looking at
your Zone 3 ticket, start queuing but the gate agent
asks you to go back to your seat as your zone has not
been called. Do you defer to their authority on principle
or trust your own expertise?

In your example, the Zone 3 protagonist hasn't actually decided that his boarding process is "better." It sounds like he is just disobeying rules (or maybe made an unintentional mistake) and no reason is given. So taking this purely at face value, Mr. Zone 3 should go back to his seat rather than causing an argument and delaying the boarding process for himself and all of the other customers.

Let's make some additional assumptions based on what seems to be your intent. Let's assume that Mr. Zone 3 has expertise in this area, and has decided that he knows a better way to board the plane. (This might be true! Airlines are experimenting with this stuff all of the time. I don't think the "best" way to board is a rigorously settled matter...)

However, in that case, Mr. Zone 3 is still wrong and should STFU and sit back down.

He might be the world's premier expert in plane boarding, but his superior method is not going to realize any gains if one rogue passenger attempts to implement this new procedure in the god damn middle of boarding. Certainly, the premier expert in plane boarding should realize this. And the gate agent is not in a position to make changes, even if he shows up to the gate early and Mr. Zone 3 makes a really great case ahead of time.

There are zero short-term scenarios in which Mr. Zone 3 is going to get this plane loaded any more quickly relative to the (in his view) suboptimal routine already in place.

He should get some kind of job working for or advising airlines if this is truly a passion project for him.

Also, in reality....

I've seem people honestly make this mistake and have made it myself. Because the boarding agent has no idea what zone you're in until you actually reach the front of the line they are not going to notice or even give a shit that you're boarding at the wrong moment. They will do their own calculus if they do notice and will surely just let you board anyway because sending you away (and risking an argument) is not going to get the plane loaded more quickly and will almost certainly slow things down. They just want the plane loaded, and their day to go smoothly, and not have to deal with complaints and look bad to their boss.

I think the logical endpoint is rules and obedience
are evaluated in context rather than with an authority
bias heuristic.

Sorry to semi-humorously pick on your example. I know it was just an example.

To your actual point I often have violated rules that I felt were simply dumb or shouldn't apply to me, when I felt that there was no downside to doing so for myself or others.

But:

1. That's not an autism-specific thing, by a longshot.

2. I didn't get the impression the linked author was talking about the sort of nuanced decision-making you describe. The linked article was a way dumber, less correct, and more harmful assertion that NeuROtYPicaLS LoooOOOOveeeEEe AUthorITY and that those on the spectrum just can't handle authority ever and can't be expected to, maaaaaaaaan. The author hedges his bet by saying those on the spectrum can't handle "blind" authority, but never defines what it means, and it seems to just include all authority more or less.