Well, deodex makes it easier to mod. When the Rom is odex, you have 2 separate files. The .apk file and the .odex file. The .odex file contains all of the smali code for the app. So, by combining the 2 files or deodexing them, you put all of the code for the apk into one file. Hope that clears it up a bit.
As for the Rom. It is completely stock. Nothing taken away. It can be rooted by simply flashing a supersu.zip our if you are using twrp recovery, it well tell you that you are not rooted and ask you if you want to install su and binaries. And it is my understanding that by selecting yes it well install all needed root files for you.