That could also be explained by the fact that there are far less In-N-Out locations than Taco Bell, so one store has to handle demand from over a larger area than Taco Bells.
If In-N-Out has the same density of locations as a Taco Bell, the per-store revenues will be quite different.
The many Krispy Kreme franchises in In-N-Out's territory had those kinds of lines out the door once too, but went bust when the lines got short.
Kogi BBQ is the epitome of this model -- they have unfathomably long lines and few locations, but spread their resources around by being mobile.
(this isn't to say Taco Bell's business is poor, I'd just rather do what In-N-Out does)
Articles like this are annoying. There are multiple ways to success, and presenting one as clearly better than others when there are so many counterexamples is disingenuous.
In-N-Out has a simple menu, above average ingredient quality, and treats their workers pretty well. All great qualities. But it's pretty evident, especially when it comes to food, that you can be bad in all those areas and still be successful, and perhaps even outcompete those who are better than you, if you focus on price and consistency, even if the thing you're consistent at is being mediocre.