Welcome to the forums. I will try and give you a bit of help, even though you are an Australian.
It's good you found that other thread. It's not so good you had the reaction to it you did, because the advice that other user received was very good. The other thread didn't "divert to the issue of tagging"... I'll explain why, because this is crucial for you to understand.
Metadata, or the data in the files' tags, is absolutely central to how JRiver organizations music. Folders are irrelevant. Where you keep things on your hard drive, is irrelevant. If you have your music spread across 10 different drives, that is irrelevant. And if you have every single music file you own totally disorganized and lumped together in one single folder, that too is irrelevant to how JRiver presents your music.
When you look at your music in Windows Explorer, the locations and folders are all that matter. JRiver is the opposite.
When you import your music into JRiver, it reads all the metadata in the files, and it then presents the music to you organized by the metadata: Album Artist, Album, Genre, etc. The location of a file doesn't matter.
If your music is being presented in an incorrect way, it's because your metadata needs correction. To put it more briefly: fix your tags. This is why the other thread took the direction it did. It's not a digression; it goes to the very heart of the matter.
An example: if two tracks have the same [Album] tag and the same [Album Artist] tag, they are by definition part of the same album. If you keep them in two different folders, because one is the 1967 original version and the other is the 2017 remaster, they are still the same album because the tags match. Change the [Album] tag on the second one to include "(remastered)" and immediately JRiver will consider them as two different albums and show them separately.
You do not need separate libraries for separate types or music or files. Your friend made a very silly suggestion. You just need to clean up your metadata. This is often the case with people who are coming from software that relies on folder organization. The tags are often a mess, because the folder organization masks the problems.
Once you have your metadata cleaned up, you can configure MC to present your music any way you want. It is infinitely flexible in that regard. But you have to start with good metadata.
This wiki article will point you at how to get started with the mechanics of tagging your music in MC:
https://wiki.jriver.com/index.php/TaggingYou can configure views in MC to only show you flac, or only show you mp3, or whatever you want. But by default, MC doesn't discriminate: music is music, regardless of location or format.
If you want to provide some screenshots of specific things that are being combined that you want to display separately or not at all, we can look at that. MC also has fields, one is called [Filename (path)], that shows the location of a file, and you can add that to a view to help you sort or filter.
A metadata error is the cause behind the problem you mention in your other thread, by the way.
I hope this helps...