You’re right, scale is absolutely an issue for companies that sell software or that are very large.
Also important to consider that most companies use software internally instead of selling b2b or b2c. Fewer than 500 businesses in the US employ more than a few thousand employees* (https://fortune.com/fortune500/2020/search/?f500_%20employee...) and there are over 17.5 million businesses (https://www.naics.com/business-lists/counts-by-company-size/).
* I may be wrong in my assumption that the Fortune 500 companies are the largest employers
There's a balance and it's more delicate than people give it credit these days. Don't get me wrong though... over-engineering and/or premature optimization is just as bad. But there is an opposite extreme as well.
At the time the scientific packages were extremely heavy and best avoided in production environments. Some people did it anyway but removed it once they needed to scale. Simply installing these packages was a huge pain and blocked one's ability to provision new machines, for example.
PyPI was indeed a big benefit. Ruby Gems are also what made Ruby so competitive at the time.