When I freelance; when I have to build a new site for my day job - this is exactly what I tell my customer / boss:
"This is Wordpress. This is how it looks out of the box, this is what I can make it look like and this is what the Admin panel looks like. It costs X to implement and will take X hours to do so.
"This is my custom CMS. It's written in pure PHP (no PHP frameworks used) and based on the Twitter Bootstrap framework. The reason no PHP frameworks are used is so any PHP programmer can come in and pick up where I left off. Every single page of the CMS is custom coded to the front end page it controls and nothing exists that doesn't need to be there. My custom CMS has been in development for years; constantly improving it as I've grown as a programmer; it's very easy to use and well documented. It costs X to implement and takes X hours to do so."
"How do you want to proceed?"
My custom is usually double the hours and double the fees - I explain everything; show past examples of both and let them decide.
If your not customizing a CMS to the customers needs (be it wordpress or your own home grown) your not providing a great product, IMO.
Sometimes, there is software that solves a particular problem particularly well.
For example, it would be relatively straightforward to design a CMS/site builder that was really great for creating landing pages. It might not do ecommerce at all. If you want ecommerce, it sucks. If you want landing pages, it is amazing.
There are TONS of CMS's out there that do just that. They don't always call themselves CMS's anymore. Think Shopify, Unbounce, and even Hubspot. Under the covers, they are generating web pages and making it easier to manage a particular kind of content. None of them markets themselves as a CMS.