I don’t really know what you mean.
But I’ll try to answer what I think you’re asking.
YouTube is a directly negotiated licence - ie it doesn’t fall under any of the statutory blankets, and is licensed territory by territory. Most rights holders are able to license for multiplied territories and often globally. But if soemthing was not licensed for a particular territory in which you were based you would not be able to watch the music video.
The recording and publishing need to be separately licensed by the record label and publisher(s), with the performance and mechanicals handled differently, and potentially flowing via a CMO or mechanical licensing society. The video will be provided by the record label - and they generally own the copyright in the video as a work for hire. If there are sample in the recording they will have been cleared by the label for both the recording and publishing. If there’s an interpolation of a song that will be negotiated and licensed with the publisher(s) or writers as a derivative work.
YouTube uses Content ID to identify the works being exploited, and uses that to account to rights holders.
Is that what you were asking?
Yes, you are of course technically correct, the best kind of correct. I think you are describing a nightmare, brother. You are describing hell.
I didn’t say it was a perfect system. I often say, professionally, that the infrastructure around music rights and licensing is insanely complicated - and as you have personally experienced it can be very frustrating, confusing and dispiriting for creators. But I’m not really sure what the alternative would look like.