I'm not sure if Shellstyle.dll will "override" certain values from MSSTYLES files. But what exactly do you mean by same structure? Because from a binary stance, yes they are, since msstyles are just DLLs with a different file extension.
But as far as the layout goes, then no, they're not the same. I've never heard that shellstyle.dll will override values from msstyles files, but if that's true then maybe you could try importing some stuff from an msstyles file. Although I'm not sure how that would work with the msstyles' CMAP.
Also keep in mind shellstyle > UIFILE > 1 only affects the FolderView, not the entire window.
as far as I know shellstyle is used by GDI system for window layout
the version in system32 folder is for classictheme
a different version can be loaded by a msstyles/uxtheme.dll from a theme folder like Windows\resources\thtmes\aero\ this is to make a custom GDI layout for the base that uxtheme.dll will skin on top of