Its because the default cfg doesn't have the USAAF option in it, only USA. But it does have a default German option, that's why the German missions show up when working in the normal install. You asked if its possible to get everything into a single, simple install. The answer is in your previous statement, "Country.cfg files are specific, too...". Modify your default cfg by creating a new option for USAAF. Copy the entire USAAF section from the DT cfg:
[country.7]
name=US Army
short_name=USA
nationality=USAAF
heading=oclock
and paste it into the default cfg. If your defo cfg is already using country number 7 for another nationality, you have to change the new USAAF option to a new unused number. If this is the case, then you will also have to go into the missions with notepad and change all USAAF allegience numbers to your new number, beginning with the header info in every DT_USAAF mission:
[mission]
version=2.0
title=%title_string%
summary=%summary_string%
objective=
intelligence=
mission_type=2
allegiance=7
total_goals=1
player_aircraft=3838
player_aircraft_name=%player_aircraft_name_string%
airfield=%airfield_string%
date=1/7/1944
time=12:00
...and then working your way through EVERY individual mission - German and American - to change all unit entries for the Mustang flights from 7 to whatever your new number may become:
[unit.16]
id=9094
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
[unit.17]
id=9095
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
[unit.18]
id=9096
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
[unit.19]
id=9097
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
[unit.20]
id=9098
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
[unit.21]
id=9099
type_id=3838
allegiance=7
skill=3
aggression=2
payload=0
....of course, if your defo cfg isn't using the number 7 already, you can just add the country number under Allies and not have to bother with all the editing.
After you master this portion, there's more details on how to merge the other stuff into your main, like the scenery, weapons, gsl and uires screens. You can even go a step further and add USAAF-specific ranking and medals for campaigning (the defo American setup is completely aligned for USN ranking and awards).