In the Net::FTP docs, site is listed under methods because its use is supported. quot is listed under "methods for the adventurous" because well, it can be troublesome...

My copy of the Net::FTP docs says:
"WARNING This call should only be used on commands that do not require data connections. Misuse of this method can hang the connection."

Both methods use Net::Cmd's command method to do the dirty work. site uses it to send the FTP SITE command followed by the quoted command as the arguments. quot uses it to send the quoted command as is.

Disclaimer: I have studied the code of this module extensively over the past six months. I briefly reviewed the code today to verify my beliefs but it's been a long day and I may have inadvertantly misstated something here.