For me, both menus have the same folders, but the Metro apps show up separately in the "Apps" folder in CSM.
My Win 10 is made from continuous updates (not clean install) starting from Win 8.
There is one thing about icons, in that they will look different depending on what size/color bit they are displayed. See picture
Sorry, I don't know how CSM relates the folders and items from Win 10 start menu other than the
C:\ProgramData\Microsoft\Windows\Start Menu and C:\Users\name\AppData\Roaming\Microsoft\Windows\Start Menu
When you say taking icons, I guess you mean making/ deleting icon shortcuts because getting access to the original icons in the .dll files is not happening.
Resource Hacker used to be able to open Win 10 Taskmgr.exe,shell32.dll files to see/change the icons inside but not anymore!
About instability
I just have to live with an unstable evolving operating Win 10 system.
I don't do any modifying/deleting of any system files/folders. Most problems in the system show up and then go away with later updates.
Example: For about a month or so whenever Microsoft Edge explorer was closed, all icons on the desktop would flash refresh, then do it again one second later.
Then eventually an update must have fixed it from refreshing for I did not alter any files/settings.
When I upgraded to Windows 1903, the glass color on CSM start menu did not work anymore, then a Windows update fixed it.
The same thing with auto sleep not working anymore, then another update fixed that.
So, Microsoft is always breaking something/ fixing it later.
There is one issue that happens a lot for me on Windows 10, though I don't know if Classic Shell has anything to do with it.
When I have some folders and lots of programs open, Windows Explorer decides to refresh and close the open folders.
I then have to open all those folders again.
Happens zero to a few times a day. Nothing is lost, just have the annoyance opening all the locations of folders again.
Very occasionally Windows Explorer closes everything, restarts itself with a clean slate, losing any work I had.
The system has hardly ever done a full crash-restart, so I'm happy about that.