I guess that it really depends on what happens with these files AFTER they have been uploaded. It doesn't matter at all what is in the file that is being uploaded... It will never be executed in your code. Unless you are at some point exec()'ing the contents of the file (ps. NEVER NEVER NEVER exec use supplied data!) then the contents of the file will stay just as they are: the contents of the file.
If somehow the file was being placed into a portion of the web server that WAS accessible, and the file was executable, then you would have a different story on your hands, but you did say that it would be stored in a non-accessible directory as well.
Given what you've told us so far, you appear to be safe as written.
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