Not sure what you mean in terms of WEBGUI command line?
There is no restriction, but you may want to optimise your rtorrent config. See this guide on the rtorrent project with regards to performance tuning - https://github.com/rakshasa/rtorrent/wiki/Performance-Tuning
Yes you can install additional plugins. Just follow the instructions that the plugin authors provide.
Just note that if you rerun rtinst main script, you will need to reinstall any additional plugins, and will lose any config changes, so if you do make significant changes to the configuration of rtorrent and/or rutorrent, make sure you backup those config files, so you can easily reapply them if needed.
Any additional programs you want to install, should not impact the installation in any way. You can add in things like Plex or OpenVPN, without any conflict.