Is manga censorship in Western countries always done with author consent?
You are over-thinking it. I guess we only talk about official localizations here, since in non-official ones, anything can be done.

When an official localization is made, some kind of contract is being signed between the possessor of rights for the manga (the author, a publishing house, doesn't matter), and the company that is going to make the localization. 

Since this contract is an legal document, it covers, among other things, the limitations (if any) that will be set for the localizer. Obviously, since different countries have different laws regarding nudity in press (as in your example), the contract should probably have clauses that regulate such possible changes (censorship or decensorship). 

Whether or not the author himself is aware of this, depends. Sometimes the holder of the rights will inform him, sometimes it will not. For example, when official localization of Spice and Wolf into Russian was being made, the author himself didn't know about it, since it was the publishing house who was holding the rights on the manga, hence it was regulating all the localization aspects. 

And after all, if the laws of some country forbid, for example, nudity in press, then there is no choice. You either change the manga to meet the laws, or it is not going to be published.