Sorry for the confusions, let me clarify things. The guide about W3 TOTAL CACHE that we provided here is actually the settings that we recommend and it works (well, not for all).
You see, not all sites have the same setup, you might have a plugin that others don't, others might have a different server configuration than yours, a lot of things come into play when tweaking a site performance or in general, so we can not really guarantee what works for you, will work to others and vice versa. And those are the sites that we are suggesting to exclude the Pro (or X) files so it does not get caught from a minifying/caching issue.
Even some caching documentation has warnings that tells you or something along these lines.
Configuring W3 Total Cache: Advanced Minification Settings
Yes, that is correct. Christian's suggestion is for X theme.
Hope this shed some lights,