The gold standard is a great checklist but there are two things to keep in mind about it. First, while it's verbose the vast majority of it are obvious things a web developer would have to do anyway even if it was an Angular directive, an OpenSocial widget, an Ember component, etc. Second, it's important to follow the checklist in its entirety when creating web components for public consumption. For instance if you're building a component for your own web application you may not really care about local effects or some of the other items.
Also the OP says it may not make sense for small sites to use web components but that also doesn't make sense. Here's the quote: "I’m not convinced either, that every company should come up with custom elements for all the things, just because they can. Most elements can be built very well with existing HTML, without costing as much design and development time. I feel many web projects will hardly have a use case for utilising custom elements, or the budget for creating them. They would overcomplicate things. It still feels like eating a 5 course dinner when all you wanted was a salad."
The problem here is that most web components are just composites of plain old HTML and some styling and JavaScript to create a re-usable piece of a layout; this means they can be done "without costing as much design and development time" but the OP purports the exact opposite. I'm not sure why (perhaps the OP equates custom component to replacing a browser native component like a drop down? Though if so that's a very specific and specialized, custom component and doesn't really fit the wording used).
There are plenty of issues with web components. Speed and the insane amount of additional connections they require are the big ones in my opinion (yeah you can combine them but there isn't very good tooling around that; even if you're using Polymer vulcanizing requires specific pathing and doesn't always work even on Google's own components) but this article really only raises valid concerns if you're going to be publishing generic components for public consumption but even think I think it far overstates the issues in that area.