Don't know that there's going to be one tool to accomplish what you want. But by combining, you may be pretty close. Directory tools, comparison tools, duplicate file tools ...
Take a look at Altap Salamander (shareware) & in particular it's Compare Directories utility. Compare can use various methods or combinations; size, date/time, attributes, contents, & subdirectories.
So if you have two similar trees that you are looking at, it can quickly filter out those sections of the tree that are identical (based on your comparison method) & then start comparing the different trees that are left.
Two top level dirs. R: & S:. R: is kind of the Source, & S: is kind of the Backup. Originally they were the same, purposely duplicated, but over time there were additions to R: & otherwise rearranged & cleaned up.
The highlighted (red) directores are not identical (per my comparison method), so deleting any of the S: directories that are not highlighted will only remove duplicate directory trees.
A#1, _from_USR, beat, bla, black ... all can safely be deleted.
Now, _from_C is different (highlighted in red).
So if I jump into the _from_C directory & run another Compare, again the difs are highlighted & those not can be deleted. So again I can safely delete from S: _ecclectic, _Instrumental, 12 Girls Band ... Now some directories are entirely new in R: & not in S: at all, like _flv & 10cc. And again some directories are different. So if I jumped into the corresponding _metal directories & Compared from there, I would come up with more diffs. In some cases I may have added an m3u or a screenshot (jpg) that didn't exist before, causing the diffs. So essentially the same, but a thing here or there that makes them not actually compare. And once you got into the bottom level directory in a particular tree, what the differences are becomes clear (usually). (With MP3, MS, WMP has a habit of messing with MP3 tags, which will both change the file date/time & contents, but not necessarily the size. I never use WMP because of that.)
Anyhow throwing a tool like Salamander into the mix (of various tools) I feel can be worthwhile. (Not to mention that Salamander is an excellent file manager too.)