In my case, I never had this problem because I originally had my hard drive partitioned, with a different System Folder on each partition. But I grew weary of all those partitions so I moved all my system folders onto a single partition once I reformatted the drive. What that means is, I just copied all the data over. I did not reinstall each OS. Because of that, I did not have the same trouble as you are having.
But thinking about it logically, you simply need to prevent the OS installer from copying files into an existing system folder. Clearly, renaming the System Folder to something else is not enough. It must be sensing the "System" and "Finder" files. So try renaming the System as 1sys and the Finder as 1find and then do your install. If that doesn't work, then compressing the entire system folder will do it, but on an SE/30's stock CPU compressing and decompressing will take a long while. Even so, it will prevent the files from being touched in any way.