We do not use PHP in anything in Webmin or Virtualmin. There is some generated PHP in a couple of circumstances (php_info display, maybe some config stuff, and any web apps that need PHP files for configuration in Install Scripts).
I’m not sure what a 3G file would do in File Manager. That’s a lot to ask of a browser timeout, but the File Manager will probably try to do the right thing and keep a spinner going through the whole thing. But, for really huge files, maybe use scp and unzip it in an ssh session, maybe started under screen or tmux if it’s really important.
Also make sure whatever user you’re uploading as has a quota large enough to accommodate that monster file and the uncompressed result.