Essentially, Becker is wondering whether you can compare tennis eras or not. And that is a question that cannot be answered. It is the same in any other sport (e.g. is Messi better than Maradonna?).
What is evident however, is that Federer (just like legends of the past such as Borg, McEnroe, and Lendl) is an exceptional talent. And talent is time-independent. It is likely that Federer with his unique talent would've won titles in the "wooden" era as well. But would he be able to beat Borg and McEnroe? No one knows.