I agree—it really does. But with help from others I’ve learned it can be defeated. Of course, for you, you’d have to put even more time into organizing and tagging after you’ve ripped than you’re already facing. Before I go further, I’ll just say “don’t try it any other way” might be the better answer. 
Let’s say you want to alter the contents of CDs within a multi-disc set… Say disc 1 and disc 2 both have four tracks, and you’d like to remove the first track from disc 2 and make it the 5th and final track of disc 1. I would do this by altering the track and disc values in your tag editor to create your virtual CD set, being as fastidious as you can be so you don’t leave behind anomalous values, and making sure your file & folder structure match up with your desired outcome.
The key is to properly configure Roon’s Import settings before you import your virtual CDs. You want Roon to obey your tag values rather than whatever it has in its database. Here’s what I would suggest.
Or, for simplicity, just set all the switches to ‘Prefer file.’ (Of course, you have to remember to set them back to what you prefer for your regular imports.)
I’ve found that chances are high that Roon will still make the proper match between your virtual CDs and the real recording in its database and fill in the appropriate metadata. I haven’t done this much, however, so you’ll have to see, and it’s possible some cleanup will be necessary in some cases.
As a quick little test, I just took the 2-CD set, Will The Circle Be Unbroken and edited tag values for the last track of the first CD to make it the only track, Track 01, on a virtual, third CD that hadn’t existed before. (I decreased by one the total number of tracks for the first CD.) After forcing Roon to rescan the library, the new, 3-CD “Circle” showed up as I designed it. Because over the years there were in all three different iterations of “Circle” recordings, Roon pulled their different album covers and assigned each one to one of my virtual CDs, even though the CDs all belonged to the very first Circle release. I had titled the CDs something like Circle 1, Circle 2, and Circle 3. When I changed these titles to Circle CD 1, Circle CD 2, and Circle CD 3, then Roon assigned all three the same, proper album cover. It wasn’t that Roon didn’t know that these three discs belonged to the same album—it did and presented them as such before and after the titling change. So, there are hard to predict subtleties like that.
Something I should point out is that in my example, I was changing the structure of an album that was already in the Roon library. Each time I make a change to an album in the library, on my computer desktop I move the CD folders out of the music library folder and then have Roon rescan the library. And then I have Roon clean up the library. Then I do the tag editing, move the folders back into the music library folder, and have Roon rescan the library. This is to make sure Roon forgets about the album before I import a modified version. I’m not sure if that is necessary, but I have the feeling that it helps prevent complications.