Both opinions are right as i see it. The problem i have with the SDK: Using the Country Config File webpage is that it only details the formatting of the country.cfg file and doesn't go further in explaining its inherent relationships with the allegiance designations in dp's, cmg's and mission files, which is the point Dirty is making.
Now, as i understand it, "3" is the default nationality number that the sim engine respects. Any country under this number will be treated as the "first nation". So, using JapLance's example above, sure, you can change the country numbering order around to present a customized default country of Italy for an MTO install, complete with all of its screens and backgrounds shown first. But if you stop there, what happens within the sim when you load an Italian campaign -- set to country allegiance "6" for example -- with Italian aircraft, vehicles and ships all still using the same old country number of "6" in their dp allegiances and the US objects are still using number "3"? Will the sim CTD on loading? If not, then Dirty's post, although very insightful from a structuring point of view, is inconsequential to avoiding disaster, but still pertinent to keeping the "house" in perfect order.
I know from experience that you can play single missions in this 'mixed-matched' way with no problems, but i was lead to believe that this kinda thing could adversely affect campaign play when allegiance designations of aircraft, ships and vehicles are not perfectly matched up to the country number. This was presented to me the first time in the old "Polka Dots" USMC Korea campaign download and the Fox Four campaigns which came with their own customized country.cfg's to prevent the loading CTD's that would occur from this mix-matching.