Actually, there's one method, the times between each craft.
The bot system needs to be designed to start up the new craft, and from what I've noticed at least, some are very interesting in the way they handle the time of that. The one I was able to catch doing it in Eulmore had exactly 15 seconds (I checked timings myself, over multiple crafts that it did, it was very VERY consistently around 14.8-15.2 seconds, which I'll argue to my own human error) between the craft finishing, and the first action of the new craft.
Now, I don't know much about crafters, outside of being an omni of course, but humans aren't exactly known for having both extended waits AND perfect periods consistently for something like that. You'd think if it was somebody crafting with enough attention for a consistent time between start and end, that they'd be doing it earlier than 15 seconds of waiting, as it only takes 2 or 3 to actually get back started. And if it was a player just afk macroing, they wouldn't get consistency on the wait time at all, as they're... afk macroing, they aren't there to click to continue the millisecond the craft finishes.
Sure bots could just go against that later on by simply randomizing the wait time, but... at least for the moment that could easily hit some of these heavy ones, some carrying probably billions of gil.
Also, I can only speak from my experience checking bots as ban waves happen, and this is what I've noticed.
If a bot is simply doing automation, and nothing else, as in no teleport hacks or whatever, then it never seems to go away.
However, if a bot does do these things (go under the ground, teleport around, etc), then they usually seem to go within 2 waves of my report.
Even just with these map bots, I've managed to track where and how some act. Any I confirmed were under the ground (/idlecam is great for this) were banned, while the one I have found that doesn't and just runs between the market and the bell has had no action taken on it.
Which comes to a conclusion that they do in fact act, but only if it actively cheats, rather than just automates.