You can do it using advanced tracker options:
https://support.tixati.com/individual%20tracker%20options
For example this:
sometrackerurl.com
header:%0D%0AUser-Agent: rtorrent/0.9.2/0.13.2
peerid:-lt0D20-
xfer_peerid:-lt0D20-
should change (both peer and tracker) peer id only for torrents with sometrackerurl.com
Peer id is 20 character long, if you'd like to have fixed peer id just fill remaining characters after
-lt0D20-