If you look at icons2.plist, you can see that TF is retrieving the icons to display for Movies and Pictures directly from macOS from the resources returned by calling NSMediaBrowserMediaTypeMovies and NSMediaBrowserMediaTypePhotos. These system calls return the icons that Apple has squirreled away somewhere in the bowels of macOS, so in this case, they aren't in the CoreTypes bundle. As you noted, these do not look like the CURRENT folder images you see when you look at the folders in Finder, these are the older deprecated (discontinued) images Apple no longer uses but has left in for any old apps that are still programmed to expect to find them in certain location, but current macOS no longers uses them.
The current 'color' icons Apple displays in Finder that I think you were expecting to see in the sidebar, are those mono color (bright neon blue in El Cap) image of a folder with the subtle 'watermark' in the center that is supposed to remind you of Music, Pictures, whatever. IMO, these are ridiculous, as from a distance or if the image is small, the watermarks are so faint, I can't tell any of them apart, every dang folder all just looks the same bright neon blue rectangle.
I believe the developer chose NOT to use those for his 'color' icons for that reason, you can hardly tell them apart at a quick glance. Rather he chose to use the older icons that date back from when Apple still had color side bar in Finder (Snow Leopard?). They were unique and distinct. you could instantly identify a folder by its icon without reading the label. I don't have a copy of Snow Leopard to fire up anymore, but I suspect the icon images you see in the sidebar now for Movies and Pictures are the same ones from back then when Finder itself still had color. I'm not sure where the specific graphic files for those old Movies and Pictures folders are stored, but they are retrieved from the system by calling the NS function calls I mention above. They are probably archived in a nib file buried deep somewhere in macOS, so you can't even access them directly anymore. A nib file in macos is a compressed file (like zip) that holds app resources...icons, images, sound clips, etc. Think 'old junk drawer' in this case, and you've got it!
The image for Desktop that TF shows by default is coming from /System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/Displays.icns. It's the same icon Apple uses in the system preferences panel for 'Displays'. TF is just pointing to it. The rest, as I said before, I'm pretty sure come from CoreType.bundle, the icons2.plist documents exactly where each color icon is coming from that TF uses by default when you enable sidebar color.
BUT REGARDLESS, if you don't like the particular icons TF is using by default when color sidebar is enabled, you can point TF to your OWN custom icons. Create a copy of icons2.plist, edit it, and name it .totalfinder-sidebar-icons.plist (include the period at the beginning, this will make it a hidden file mind you so wait till you are done editing before you rename and put the . in front).
Place the file in your home folder. TF will look for the file when it starts and use the icon info there to retrieve the images YOU want displayed. How to edit: For example, if you want to change the icon displayed for Music, change the line that points to NSMediaBrowserMediaTypeMovies to the path to your own custom ICNS icon file, like 'System/Library/CoreServices/CoreTypes.bundle/Contents/Resources/MusicFolderIcon.icns' or 'ThisIsMyCustomMusicIcon.icns'. If you have SIP enabled, you can't edit CoreTypes bundle, but you can put your custom icons ANYWHERE on your drive that you have access to /Documents/My Custom Icons' folder for example. Just insert the full path name to the file.
the web is full of icons to choose from. There are programs that can convert PNG or JPG to ICNS, many of them free. Even Preview will do it, with a little work. ICNS is the file extension for a macOS icon file, much like in Windows which uses .ICO file extension. Caution, don't go bigger than 256x256 pixels, may not display at all. Use 72 DPI (dots per inch) when you save your image.