That's one problem with Wordpress' default renders; it sends developers down those relatively narrow paths of customizing existing output. It's easy if requirements are flexible enough to allow that, but not the right CMS for truly customized content architecture and presentation.

> truly customized content architecture and presentation

Can you give an example of something like that which is not possible with WordPress?

Customized presentation is possible by starting with a blank template. Most do not do that, so if they want to customize, they spend time modifying and working around the default views. This has an effect of constraining the look. The difficulty emulating controller-like behavior means that adding multiple pieces of content to a view takes extra work.

As for the content architecture, Wordpress cpt are limited in their ability to relate to others and to define flexible custom fields (even with ACF.) It’s possible to hack together something like what a more flexible CMS or application framework can do, but it’s fragile and takes a lot of boilerplate, which, similar to template customization, steers the developer towards a similar architecture to other sites.

For these reasons, increased development and maintenance cost make it unlikely that an attempt to develop something truly customized on Wordpress will be successful. That said, many only know Wordpress development so may still get further with it than with a closer fit to their project.