It is true that with Shopify or similar platforms you aren't able to make backend choices or implement caching like the article has described, and yes it's true that all the themes in the theme store aren't perfectly optimized for page load time -- but the question really is do you want to do any of this stuff yourself? Shopify has invested years in their platform to make your website as fast as possible for as little money as possible. The themes that Shopify publishes in the theme store undergo huge amounts of performance testing to ensure that you aren't losing money from latency. The platform comprises a world class CDN, and Shopify doesn't charge for bytes through it. The platform uses many layers of backend caching at the data access, logic, and rendering layers to make your shop as responsive as possible if anyone has been to it before. Shopify powers some of the biggest sales on the internet that truly dwarf Good Morning America. The platform is also geographically redundant such that an entire datacenter can fail with only a moment of visible impact to you and your customers. If what I'm saying is true and you don't actually sacrifice that much flexibility on the Shopify platform, why would you choose to have to implement all the above?
Another angle is operations: How many people do you think they have monitoring it and ready to respond to any incidents? Shopify serves an order of magnitude more traffic than Baquend saw at the very peak of this occurrence every single minute of the day with a better response time on average.
The Shopify platform took an army of engineers 10 years to build so it would seem unlikely that Baquend has all the same features and stability. How much do you think Baquend charged Thinks to build this? Is it more than $29 / month?
Source: work at Shopify and built many of these systems.