Why is different the "free" as in freedom concept for documentation from the concept of "free" as in freedom for "software"?
It isn't that different, the four freedoms still apply. The difference is that the content isn't a functional work, and one may wish to attach a dedication to the text, or maybe something else that isn't related at all to the actual text.
Why does FSF have two distinct opinions about the adequate level of freedom for manuals and for software?
Because they are different. It is that simple. http://www.gnu.org/philosophy/free-doc.html
There is no doubt that free software needs free documentation, even FSF says this. If so, why does FSF allow restrictions to modifications of documentation (using FDL) that does not allow for software?
Because such restrictions make sense, you don't need the right to modify my thoughts about why I wrote the book, or to whom I dedicated the book.
There is people that thinks software is the conjuction of programs and their documentation (and other thing, like images, etc.). For example, Debian project seems to think this way.
Debian consideres _everything_ software, which is simply bogus. Some images might make sense to have as verbatim only, same applies for many texts about philosophy, or even music recordings. This does not apply to functional works, like software, where modification is an essential right.
You don't need the right to modify my poem about dragons, or infact, this text.
Why limit modification of documentation of a free program, if we do not want that limit for the program itself and if the documentation is necessary?
You aren't limited anywhere when you modify free documentation of a free program. This is like saying that you are limited by the GPL to create non-free works, which is simply nonsense.
Cheers!