Not to undermine your idea, but why are you building your HTPC with a Raspberry as its core? Seems like that might not be the brightest idea, if a requirement is transcoding.
If you want to go in this direction, I'd have RasPlex on its own, put Raspbian on the 2nd Pi 2, load it up with a torrent client and a batch transcode job to add to PMS's library.
My first goal here was to have all that running on only one raspberry PI.
But from what I've read, I can't have plex both client and server on the same raspberry PI. My only chance was to use PlexBMC... But Rasplex seems so much better...
That's why I'm thinking about having 2 Raspberry PI... Am I wrong?
Rasplex is certainly a better client, so run that on a Pi. I'd buy anything, ANYTHING else to run PMS though. For one, buy something that has native SATA ports for your media! If you already have a Windows or Linux box at your house, use that.
I'm not sure how much time you have, but any transcoding on a Pi (even offline) is going to take hours.
People forget that you can use hardware encoding on the Raspberry Pi... just have to make sure your software uses it. Good point about media though, USB2 is slow and shared with the ethernet port.
You can buy a cheap mini PC or even a used PC from Ebay for $100.
I run a server with Ubuntu 14.04. It has Plex and a number of other server systems on it for my media and files. I have scripts that handle transmission-bt and downloads are then renamed and sorted by scripts using FileBot cli.
If I need to convert something, I manually do it with either handbrake gui (when I'm lazy) or handbrake cli.