In Inn you can use the option "--with-etc-dir=PATH" to set a different etc dir for the config files. I used "--with-etc-dir=/usr/local/etc/inn" by adding this to the Makefile of /usr/ports/news/inn. 
However there occur a few errors if you use this option. The first thing is, it stops the installation process started by a "portinstall inn" as follows (a make install clean nearly produces the same output):

If you install Inn 2.4.1 with the option "--with-etc-dir=PATH" by adding this line to the Makefile it stops at install time with the follwing last output (tested on 3 Systems)

Checking for configuration files
find: /usr/local/news/etc/: No such file or directory
Creating empty history database...
makedbz: open of /usr/local/etc/inn/inn.conf failed: No such file or directory
mv: rename history.n.dir to history.dir: No such file or directory
*** Error code 1

Stop in /usr/ports/news/inn.
*** Error code 1

Stop in /usr/ports/news/inn.
        ! news/inn      (install error)



So first it looks for the default etc dir /usr/local/news/etc, what isn't correct at all. Then it look at the right place again:

"makedbz: open of /usr/local/etc/inn/inn.conf failed: No such file or directory" but the conf files were installed incorrectly -> they all have the ending ".dist", which causes makedbz not the find the file "inn.conf" because its name is "inn.conf.dist". 
Even if you rename the ".dist" files manually and install inn again... then it will finish installation, but it still doesn't start because it still seems to expect the conf files under the default etc dir (/usr/local/news/etc)

How-To-Repeat: Use a system, which hasn't installed inn, yet or remove any previously installes inn files, add "--with-etc-dir=/usr/local/etc" to the proper place in the inn Makefile and run a "portinstall inn" or "make install clean". The last way doesn't provide that much information when it stops installing.