What's an example of a point where using the two atan2s doesn't do what you want? I think that ought to work...
Here's some test code I'm using:
worldRadius = 10.0
for i in range(0,10):
# choose a random lat/long point on sphere
latitude = random.uniform(-2*pi, 2*pi) # up/down, y
longitude = random.uniform(-2*pi, 2*pi) # left/right, x
# Find the real world 3D position on the sphere surface
real_x = worldRadius * cos(latitude) * sin(longitude)
real_y = worldRadius * sin(latitude) * cos(longitude)
real_z = worldRadius * cos(latitude) * cos(longitude)
# Now attempt to do that backwards and get the lat/long again from this real world position.
latitudeAgain = atan2(real_y, real_z)
longitudeAgain = atan2(real_x, real_z)
# Put all lat/longs in the range 0 - 2*PI for easy comparison
latitude += 2*pi
longitude += 2*pi
latitudeAgain += 2*pi
longitudeAgain += 2*pi
latitude = fmod(latitude, 2*pi)
longitude = fmod(longitude, 2*pi)
latitudeAgain = fmod(latitudeAgain, 2*pi)
longitudeAgain = fmod(longitudeAgain, 2*pi)
# Also try to get the position once again from the newly got lat/long
other_x = worldRadius * cos(latitudeAgain) * sin(longitudeAgain)
other_y = worldRadius * sin(latitudeAgain) * cos(longitudeAgain)
other_z = worldRadius * cos(latitudeAgain) * cos(longitudeAgain)
print "Lats: ",latitude," - ",latitudeAgain," Diff: ",abs(latitude-latitudeAgain)
print "Lons: ",longitude," - ",longitudeAgain," Diff: ",abs(longitude-longitudeAgain)
print "Pos1: ",real_x,real_y,real_z
print "Pos2: ",other_x,other_y,other_z
And the test output:
Lats: 1.57903473033 - 1.57903473033 Diff: 0.0
Lons: 5.10226596478 - 1.96067331119 Diff: 3.14159265359
Pos1: 0.0762007311343 3.80061735995 -0.0313117278778
Pos2: -0.0762007311343 -3.80061735995 0.0313117278778
Lats: 5.93480811564 - 2.79321546205 Diff: 3.14159265359
Lons: 3.39572137905 - 3.39572137905 Diff: 0.0
Pos1: -2.36299962085 3.30408958826 -9.0973998891
Pos2: 2.36299962085 -3.30408958826 9.0973998891
Lats: 2.36983896676 - 5.51143162035 Diff: 3.14159265359
Lons: 3.43495760648 - 0.293364952892 Diff: 3.14159265359
Pos1: 2.07248505761 -6.67597897677 6.86069121889
Pos2: 2.07248505761 -6.67597897677 6.86069121889
Lats: 2.71182886148 - 2.71182886148 Diff: 4.4408920985e-16
Lons: 5.72284029962 - 2.58124764603 Diff: 3.14159265359
Pos1: 4.83148051356 3.52937619571 -7.70042639429
Pos2: -4.83148051356 -3.52937619571 7.70042639429
Lats: 4.41217625779 - 1.2705836042 Diff: 3.14159265359
Lons: 3.85396423175 - 0.712371578164 Diff: 3.14159265359
Pos1: 1.9329383337 7.22964312956 2.23807587188
Pos2: 1.9329383337 7.22964312956 2.23807587188
Lats: 0.135838374462 - 3.27743102805 Diff: 3.14159265359
Lons: 1.64115450181 - 1.64115450181 Diff: 0.0
Pos1: 9.88336821577 -0.0952011605369 -0.696525460481
Pos2: -9.88336821577 0.0952011605369 0.696525460481
Lats: 5.03750570722 - 5.03750570722 Diff: 0.0
Lons: 1.46803830938 - 1.46803830938 Diff: 0.0
Pos1: 3.17734475072 -0.972036026841 0.327651707624
Pos2: 3.17734475072 -0.972036026841 0.327651707624
Lats: 0.350045505601 - 0.350045505601 Diff: 0.0
Lons: 5.436873812 - 5.436873812 Diff: 0.0
Pos1: -7.0342906832 2.27283766805 6.22558689914
Pos2: -7.0342906832 2.27283766805 6.22558689914
Lats: 0.0171541809941 - 0.0171541809941 Diff: 0.0
Lons: 1.13445981395 - 1.13445981395 Diff: 0.0
Pos1: 9.06172667879 0.0724937989497 4.22559887977
Pos2: 9.06172667879 0.0724937989497 4.22559887977
Lats: 1.69526847861 - 4.8368611322 Diff: 3.14159265359
Lons: 2.92736309538 - 6.06895574897 Diff: 3.14159265359
Pos1: -0.263938369219 -9.69580670745 1.21312953854
Pos2: -0.263938369219 -9.69580670745 1.21312953854
As you can see it works in a lot of cases, shown by the "diff" between the original and the newly gotton lat/lon being 0.0 (and Pos1 and Pos2 being equal).
Funnily, when both the lat and long are out by 180 degrees the correct position is also returned.
In the cases of failure, only one of the returned lat or long is out by 180 degrees, and Pos2 is directly opposite (negative) to Pos1.
So it's really just the sign of the represented point that wrong in some cases. The actual absolute values are correct.