You are incorrect with your assumptions.
As 'advanced' as Youtube's Reference Library is, it is definitely not all encompassing of all (or even a majority of) protected works. It covers many of the bigger labels. But dont fool yourself into thinking that its universal or that a lack of response means you have permission.
Theres simply no way for youtube to scan all incoming material for all copyright. This is because there is no ubiquitous means of doing such. Youtbe would have to be the global means of acquiring Copyright. They are able to scan material that matches what they have in their library supplied by major labels, but this is far from complete.
Dont equate them having the capacity to scan versions of works with an all encompassing method for detecting ALL copyrightten material. Many independent releases and smaller labels will not be picked up by those methods (incorporated into Youtube's Reference Library).
Any time you fix original material that meets the requirements (as defined by the region you are in) for copyrightable material in a tangible medium, you have a copyright in that work. Theres no way to know just by the fixation itself that it is an original selection and arrangement of copyrightable material. In many countries (the USA included), you neednt register a work with the copyright office to have a copyright. In any regards, registration does NOT mean youtube will detect it.
Make no bones about it, the fact that they dont remove/warn/block the content you post is in no way an implicit permission to use someone else's work. Just read Youtubes user agreement. They are not a clearing service for licensing rights.
Not getting caught doesnt mean permission/legitimate use.