Well, I'm a long-time Debian user, so I'm actually used to this system. I play with it, not against it. I use the split config option, even.
But I've just found something that you should be VERY interested in:
http://pkg-exim4.alioth.debian.org/READ ... l#id280581
Quote:
2.1.6. Using a completely different configuration scheme
If you are an experienced Exim administrator, you might feel working with our pre-fabricated configuration cumbersome and complex. You might feel right if you need to make more complex changes and do not need to receive updates from us. This section is going to tell about how to use your own configuration.
But, you might profit from keeping the Debian magic. Most files that come with Debian exim4 are conffiles. Debian is going to care about your changes and keeps them around. Additionally, a lot of configuration options can be overridden with a macro, which does not require you to actually change our configuration file. A lot of people are using our configuration scheme, and maybe it is going to save you a lot of time if you decide to spend some time familiarizing yourself with our scheme.
2.1.6.1. Override exim4-config configuration magic
If you are only running a small number of systems and want to completely disable Debian's magic, just take your monolithic configuration file and install it as /etc/exim4/exim4.conf. Exim will use that file verbatim. To have something to start, you can either take /etc/exim4/exim4.conf.template, run update-exim4.conf --keepcomments --output /etc/exim4/exim4.conf, or use upstream's default configuration file that is installed as /usr/share/doc/exim4-base/examples/example.conf.gz. You are going to lose all magic you get from packaging though, so you need to be familiar with Exim to build an actually working config.
/var/lib/exim4/config.autogenerated, the file generated by update-exim4.conf, is ignored as soon as /etc/exim4/exim4.conf is found. You should not edit /etc/exim4/exim4.conf directly when Exim is running, because the forked processes Exim starts for SMTP receiving or queue running would use the new configuration file, while the original main exim-daemon would still use the old configuration file.
G'luck!