I totally agree with you. Having all tags/notes organised in one workspace clutters the left pane of bear. The tag tree grows to an extent that makes it hard to work with. Currently there is no way to organise the tags but only by alphabetically sorting.
You misunderstood me, probably due to my bad english. As you can read in another of my posts my approach was not to prefer tags over folders but to merge their way of working. I didn’t want say: Take the tags as folders. Rather than that i wanted to point out that actually the nested tags in bears and the frequently requested folders basically are the same way to organise notes, especially when compared to cross linking and backlinking. I think that people wants to create tags BEFORE adding a note to it, so that they have a tag structure already existing: so notes can be added to these tags WITHOUT writing these tags in its fully length. I am convinced that exactly that is the feature that people mean when they ask for folders. And believe me, i know how cumbersome it would be to place inside of mac finder a file into a folder by writing the whole path. So you say there is a difference between tags and folders. My answer was: yes, there is, but rather than adding a second organisational element to tags, just merge their functionality 
I think here the power of cross and backlinking is a better way for evident reasons. When you create an own note for acid bases you have many advantages: you can write a short note about acid bases, what they are and so on; the text to it may contain links to other notes; the list of backlinks ARE the connection you desire; and if in the presentation of the backlinks the surrounding text of the crosslink is presented, then you can even see in which context the link to acid bases appears. backlinks reduces the necessity for tagging