As for the interface, I'm simply observing that using a browser (which is an HTML interpreter) to interface with FTP (which is not the hypertext protocol) seems weird*. An FTP client for FTP transfers, a browser for HTTP.
As for security, neither protocol (FTP/HTTP) could be rightly called secure. As for integrity, FTP may have a slight advantage. Speed? For most people, irrelevant; the speed of the downlink is the limiting factor, and firewalls these days occasionally create issues with multi-port passive FTP transfers, so it seems to me. It could be that this isn't an issue in your situation, of course.
Assuming that you put together a form with enctype="multipart form/data", a file "browse" input (type=file), etc., submitting the form will transfer the file to the HTTP server via HTTP POST, yes. This is what you discovered; I merely confirmed it.
To get back to your original question; PHP could serve as an FTP server, but I don't see how it will help on the client side, as it's not a client side technology... in order to do an FTP "put" from the client, something on the client's machine will have to do some work....
*granted, it's done all the time, since (Microsoft was first?) browsers added FTP capability. But I don't think there are any JS functions to do this automagically???