Avoid adding domains silently when top site file is provided

[abhi-agg]

There are some domains that are added silently while creating domain manifest.

What we want is following behavior:

1. Don't add them when top sites file is being provided externally by the user
2. Add them if top sites file is not provided (i.e. for an implicit Alexa top site list) to main backward compatibility with how the script was working before