As it is now Plex is able to create optimized versions of files. However Plex only uses them if a user manually selects this versions.
If you have an optimized version 10 Mbit 1080p and the original file is 40 Mbit 2160p Plex transcodes the original file if a user requests a 720p 4 Mbit version and ignores the optimized version. (See http://forums.plex.tv/discussion/245579/optimized-versions-for-uhd-files#latest)
As 4K files will be more common in the coming years but a lot of content will still be watched in 1080p it would make sense to be able to create an optimized version in 1080p which serves as default file for all transcodes which are requested with an even lower bitrate.
4K transcoding is really hard on any CPU and as long as high end consumer processors aren’t able to transcode multiple instances of 4K files, having 4K files in a shared library is an absolute no go.
Therefore manually having to create 1080p files and seperate them defeats the purpose of Plex.
Best regards.