Its not a bad theory but it is one that I am not sure evidence supports that inference.
First, the problems (as stated in the article) that Tesla is claiming are the primary constraint with the Model 3 are related to battery manufacturing capacity. That could potentially be related to technology/design obviously, but manufacturing could also just be a production problem. Those batteries in NV are actually built primarily by Panasonic [0]. Interestingly, that article also discusses the fact that Tesla has pulled back on plans to power the factory using a solar roof. Critically, that has left them relying on grid power which has enough power bumps (2-3/week) that it is a major production headache and is combined with labor difficulties in the factory in regards to talented and trained technicians.
Second, according to other industry sources [1] The issue is not the batteries but the body manufacturing. The body (which is also the frame in modern unibody cars and even most trucks) line is almost certainly being done by hand based on rate of production. The line isn't just not installed in CA yet, its not even fully built by the Michigan supplier. Why? Someone has to take the blame and it can be either Musk [2] or Tesla [3] because it sure isn't my fault. Toyota gives away the secrets of its internal process for free (partially as internal motivation to continue to improve...because they now must get better to stay on top) but hey they also have a full time CEO. Toyota offered to help Tesla, until Musk kept making fun of fuel cells. On the otherside there is what is happening now, with Tesla sending (confused and in flux) plans to their body line supplier a year after major OEM's sent plans for NEXT years models. Not to mention that the same journalists reported this all a year ago...because Tesla hadn't even begun the permitting process necessary to hit its own ramp timeline with the state of California [4].
Compare to their same reports on Jaguar's upcoming EV [5], It looks like Tesla continues to either (1) not now how to do manufacturing or (2) are still working to define the disruptive innovation in manufacturing that allows them to not test their production line. That disruption has escaped places like Toyota (and every other car manufacturer), Intel (and every other semiconductor manufacturer), and every other manufacturer in general who run a LOT of prototype prior to committing to production and build that time into their schedules. The other option is (3) Musk knew all this a long time ago and has been misleading folks for quite a while.
TL;DR: Tesla thought it was immune from the god given rules of running a factory. Human and robot factory employees are not AWS instances. Meatspace =/= code
Side story: One area Toyota save immense time was reducing the time it took to change over metal stamping dies from 3 days to less than ten minutes [6]. GM took a lot longer to learn these lessons [7].
[0] https://dailykanban.com/2017/10/tesla-gigafactory-solar-powe...
[1] https://dailykanban.com/2017/10/model-3-body-line-still-in-d...
[2] https://dailykanban.com/2017/07/fremont-problem-starts-m/
[3] https://dailykanban.com/2017/10/source-tesla-responsible-mod...
[4] https://dailykanban.com/2016/09/docs-reveal-teslas-productio...
[5] https://dailykanban.com/2017/11/no-production-hell-jaguars-p...
[6] https://en.wikipedia.org/wiki/Single-minute_exchange_of_die
[7] https://history.gmheritagecenter.com/wiki/index.php/1986_Die...