That was my impression of the whole thing, too. I've long had an exim configuration I could decorate my walls with, without understanding what most of it did or if it was secure.
Recently, I got so fed up I began writing my own mail server suite. It's still pretty basic and in development, but it does have some of the features you mention, namely
> SMTP
> POP3
> WebMail (though rudimentary)
> WebAdmin
> Multi-Domain support
In the pipeline, but not yet ready
> IMAP
> Plugins
Some of the goals of the project are to have a mail processing suite with a clear interface between the modules, as well as easy extensibility and configuration.
Me and some people I've talked into testing it already run some instances, and so far it has proved pretty stable.
Caveat: The backend is an SQLite database, so if your use-case is serving a lot of clients, there might be some lock contention.
If you're interested, check out https://github.com/cmail-mta / http://cmail.rocks/