Here's what they could do to improve the system:
Have well-placed, highly visible signage throughout the ordering area, pointing to the number-puller location.
Increase the visibility of the number-taker machine.
Have greeters near both entrances during rush times, offering direction to the obviously lost.
Have multiple number-puller machines that are synced to prevent redundancy. Press a big red button, your number is spit out.
Have whoever is calling out the number raise their hand, or hold up a number (digital display), so the person waiting doesn't miss their turn due to chaos/poor line of sight/etc.
Really, it's not that hard to create a kinder, saner, more human-friendly queuing system.
It's pretty clear to me that from the get-go, part of their schtick is makin' the customer "work for it" and be willing to sit on splintery crates in a dumpy parking lot (back in the day), etc.
If it were important to them to create a welcoming, user-friendly environment, they'd find a way. There are people who are experts in this -- I'm not.