Of course, LiveView isn't MVC in the classic sense, but it still uses plugs. Its goal is to simplify the SPA which I'd say it does a particular good job of.
[Edited to fix part of a sentence I deleted by accident]
Ignore the "View" modules. Put nothing in them. You can also eschew the "Context" modules for your database stuff, and just use Ecto functions directly, though, if you do get into the habit of using Context modules, it will make your life easier to have a unified point of view that abstracts away, e.g. caching, or, if you decide to go full CQRS/event-driven, if you need to send a copy of your data to a datalake, etc, etc.
Actually LiveView tends to have less module-indirection than "deadview"s.
If you prefer to have simple apis, you can just drop phoenix altogether and just stick to Plug. This will give you a ruby/sinatra-style experience that may be more your style, and, IMO, a good way to learn elixir. I did this for a long time before finally giving in and learning phoenix. I turned out OK.
And having to go through a few files to understand how a request is handled is not out of the ordinary in an app, especially if it's grown over the years?
For example:. What exactly is the distinction between an endpoint and a router?
You can have multiple routers. I just built a thing where foo.com uses one router for the main site and *.foo.com is something else.