Have done a few turns through e-commerce over the years, and I agree 100% with you.
That said, in the context of a Marks & Spencer-sized company (~$13B revenue), it absolutely can be a competitive advantage to in-house e-commerce if it is resourced & staffed appropriately. They are talking about a £300m hit to profit, so they appear to have some headroom for running a complex site.
Doing in-house gives the opportunity for a company to fix the kinds of things you mention with dodgy plugins etc. It also lets them take advantage of Doing Things Our Way, which sounds silly until you consider that Doing Things Our Way is how they got to be so big. And of course, in-house builds are still allowed to use off-the-shelf software where it makes sense.
Also DIY allows companies to adopt new stuff at their own pace. This tends to be important at times of tech transition like it appears we are now reentering.
Will reiterate that e-commerce is hard & there are really no easy answers.
To be clear, I definitely agree that retailers on the scale of Walmart, Target, Home Depot, Macy's, etc. (probably M&S then? I don't know Britain well) probably have the budget and justification to in-house the ecom website if they have the appetite for it, and indeed, given how unique their needs are are relative to the median site served by the likes of Shopify or even the average customer of the "enterprise" platforms like ATG... they're likely to be able to see a positive ROI on it, unless they screw it up big time.