First, node-red does not install to this location. This location is created only after you launch node-red. The .node-red directory is where flows are created. This does not exist until node-red has been started.
If you want to avoid the automatic creation of this, simply pass in a user directory when starting node red.
Second, there are almost almost zero reasons to install as root and MANY reasons not to (you will find this out when attempting to install modules etc). Also, when it is installed with the -g option (like the installer script does), each user launching node-red gets their own user directory, by default in their home directory.
So if you want multiple node reds running under the same or different accounts, then just launch node red with the appropriate command line parameters that sets the user directory and the port.
This may help : Node red multiple instances - #7 by Steve-Mcl (it is windows based but should give you the general idea)
Lastly, if you want to run multiple node-red, by far the simplest way is to install something like FlowForge. It does all the work for you, in a nice neat tidy web based frontend. You can add multiple users. You can add multiple node-red. Up to you of course.
(Full disclosure: I work for FlowForge)
