Well, the answer is, the badly defined MBOX format is the reason.

Certain mail delivery agents (MDA) and POP3 server implementations do have different interpretations of the MBOX format. In fact there are numerous MDAs (even procmail) out there which do not correctly escape those "From " line appearing in a message body and for that reasons most POP3 servers just plainly delivers the messages out of a MBOX format 'as is' instead of removing the ">" escaping. And unfortunately that missinterpretation is so widely spread over the various MDA implementations that a proper fix for it is really hard - if not impossible.

So, the answer is that this quoting is already done during initial mail delivery and that most likely your ISP is to blame for it. The only sensible approach to finally fix these common ">From " quoting issues is to force your provider to switch to the better defined and well accepted maildir format which doesn't depend on that '>' escaping...