clover is actually wrapping explorer.exe (and from my testing, causes SYSTEM instability not just when using windows explorer) things like desktop work area are hard-coded in (in my case, with my 4k monitor, the taskbar is at the center of my screen, unless i set my resolution to 1920x1080) along with other various lockups. You may find it more stable, but if you notice any oddities I would start with clover.
It should work fine with explorer toolbars, but I think classic shell is trying to hook explorer.exe (and instead seeing clover.exe and not activating)
In-theory you could trick classic shell into thinking clover is explorer.exe... but Theres no telling how that will play out