The big issue is browser support. According to caniuse, IE and Edge simply have zero support while Opera and Safari have only partial compliance. The current Firefox ESR doesn't support it either (behind a flag).
The polyfill incurs a big performance hit and a lot of devs need to support those browsers for several more years.
That's silly, customized built-ins are not an essential feature. They are a nice to have. You can get by without ever using them, which is indeed what most people do. As does the subject of this discuss, the Lightning Web Components doesn't use that feature at all.
It also means, that you cannot use existing form controls for your custom element, you must build them up from scratch from divs, and relegate them into uncanny valley of not-quite-native, slightly-off elements.
Yes, it is possible to not use them; you can always make your life harder than necessary, you could also write an modern OS in assembly, for example, if you wanted to. If people are avoiding them today, one reason could be that they want their components to run in Safari.
Even if you aren't able to inherit from a form element, can't you still `createElement` one and add it inside your custom element? Surely they don't force you to reimplement <input /> from scratch!
Yes, you can compose them; and then implement a proxy that creates all the methods and attributes that given element class is supposed to have and forward them to the real implementation.
Busywork, so Apple can hold their position. How nice. No, it is not "perfectly fine".
At least that is my understanding from Angular, Vue, Ionic, Svelte and plain VanilaJS point of view.