I think you should take a closer look as to how these modules work. I haven't worked with File::Temp in a while, but, if I remember correctly, it's purpose was to create a file with a random or semi-random name that would go away the second the program is completed. The module considers the filename to be mostly irrelevant because it doesn't know the filename when the program starts. File::Copy, however, works mainly under the assumption that you know what the filename is.
The warning in File::Temp is mainly for security purposes, so a hacker can't be just watching for the existance of a particular file, and attack. For example, if you had a Perl program to do a mass insert into the passwd file on UNIX, it wouldn't be to good to have a fixed file name that a hacker could intercept and add to during an update. It's also to prevent race conditions where you would have multiple process potentially creating a similar temp files at the same time. I'm not a security expert, but if you have one singe-threaded process copying a single file to a temporary location, I cannot see where using the filename from File::Temp would be a problem.
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