Hi,
I think You have several options to solve Your problem:

1. Allow multiple instances of jEdit (multiple JVM's):
At the command line which invokes jEdit, You have to omit the "-server" switch.

2. Use multiple jEdit views:
- see http://www.jedit.org/users-guide/overview.html
- Generally this should be the better way to get multiple jEdit windows.
- If You want to see different set of buffers in the views (which seems to be Your goal), than You have to set the Buffer Set scope to "View" or "Edit Pane" ( http://www.jedit.org/users-guide/buffersets.html ).
- In each View You can activate a different project!

3. Multiple Projects
I don't understand Your problem: If You have more open files than You like, why would this be better with multiple projects open?
Anyway, in Project Viewer You have the ability to chose a group of projects instead of a single projects (there is at least one group "All Projects"). Then the plugin dockable shows all projects of that group. Where is the difference for You between an active group or project?

Robert