It is the same but with a different precision, which is more clear with more digits:
x = N[9999999966650702/10^16, 50];
y = N[-6618533197939224/10^28, 50];
z = x + I y;
Arg[z]
Precision[%]
ArcTan[y/x]
Precision[%]
ArcTan[x, y]
Precision[%]
Im[Log[z]]
Precision[%]
-6.618533220011567667706532393335254203668654848053*10^-13
49.699
-6.618533220011567667706532393335254203668654848053*10^-13
49.699
-6.618533220011567667706532393335254203668654848053*10^-13
49.699
-6.6185332200115676677065323933352542037*10^-13
37.9713
as you can see the 'log'-route costs more precision. Why exactly? it depends on how Log is calculated internally. Log might be optimized for a different range of numbers compared to Arg and ArcTan. Note that the 'angle' is very very close to 0. Such that y/x = ArcTan(y/x) very closely which might aid in finding higher numbers of high precision. A series expansion of Log around {1,0} in complex plane gives a similar answer, but with higher precision:
Series[Log[\[FormalX] + I \[FormalY]], {\[FormalX], 1, 5}, {\[FormalY], 0, 5}] // Normal
Im[% /. {\[FormalX] -> x, \[FormalY] -> y}]
-6.618533220011567667706532393335254203668654848053*10^-13
Always try to use the function that is intended to do the job. If you go a 'long route' it might costs you precision in each step...
Second thought: Log calculates both the Real and Imaginary part:
ReIm[Log[z]]
{-3.33492980556087817880253613684648132101666*10^-9, -6.6185332200115676677065323933352542037*10^-13}
Could it be that some precision is 'lost' in the real component? I'm not sure if that is possible, but I could imagine that there is a balance in precision for each component somehow...