When it loads, Cities XL reads some files first and foremost .class files are part of it!

If you uncompress every files of the game, you will find them in : data\design\buildings (for buildings for example).
A .class file refers to a SGBIN file which has the same name. These are editables (XML) text files.
There are other references to other files but we will speak about it in the SGBIN Tutorial.

All that to say to you that Cities XL cannot read several files with the same name (SGBIN, .class or even textures files) without replacing them. So, if you modify a SGBIN without changing its name (and all files names inside + modification inside some files), if you create a patch with this SGBIN, the original object will be replaced.

On the contrary, if you change its name (with this tool) and that with your patch you add the necessary files, a new object will be created. It will always be the same 3D shape, but its textures will differ, and his properties also if you changed them in files envisaged with this effect. (see SGBIN Tutorial)