A file copy of the contents is not a preservation of the original media in its entirety. There might not even be any "files" to copy, depending on the platform (many Amiga games would bypass having a filesystem entirely and access data in a raw, direct manner).
Working with disk images allows recovering "deleted" contents, or otherwise recovering data from "slack space" (say, if a file was edited and shortened, the data after the new end of the file in the final sector is likely still present).
Also occasionally the original floppies contain interesting information in the unallocated space of the FAT filesystem – remnants of deleted files left over from the development process.