Andrea, below is my opinion.

1. What do you think about it? Is it
better to put it back in the body of the manual, in the corresponding
section?
I like it separated as "Real World Usage" like you put it.  But I would add an explanatory beginning that mentions the YouTube videos and that this section may have links to videos.  This way those people who actually made a hardcopy print of the manual are aware that these are real-world examples with links.
2.  Do you like the idea of
 
integrating the manual with explanatory video links or is it better to
keep Manual and videos separate?
Originally I was somewhat skeptical of putting in the video links (just like in the case where people may print this out) but I think it is quite useful in providing conceptual usage that some may not have even thought of.  For example, GG and I had no idea that fary54 was using OpenEDL in his scenario and it helps us to understand why a specific request to make something work differently is useful.  Similarly, use of Proxy was completely mysterious to us because it seemed totally unnecessary.