Similarly, the cfx file is not a configuration file, it is a list of instructions on how to change existing cfg file.
Each <section> takes a modification directive (blank, "edit", "clear", "delete", "overwrite") that applies to the following sections.
So if you have a threshold that you don't want changed instead of the typical
<section> overwrite
threshold=78
</section>
You would use
<section>
threshold=78
</section>
because no directive specified means "add if not there otherwise leave alone".
And because the cfx file isn't a cfg file, there's no limit on the number of times a section can occur.
It does get trickier on the probes that automatically configure themselves - like allowing cdm to auto detect filesystems but that's not impossible to achieve.
One alternative is to script the process of applying the customizations - or scripting the cfg deployment instead of using packages.
-Garin