Untested:
RewriteRule ^([^/]+)/([^/]+)/([^/]+)\.php$ $1-$2-$3.php [L]
I can't really understand your explanations about virtuality and existence: one-two-file.php must exist or you'll have nowhere to redirect to.
Update
The previous version works fine when used from an .htaccess
file. However, if used from main http.conf file you need to add leading slashes:
RewriteRule ^/([^/]+)/([^/]+)/([^/]+)\.php$ /$1-$2-$3.php [L]
I presume that's why it wasn't working for the OP (he was probably getting a 404 not found status code).