The Project Modular Area is the modular root MUX of your project and shows the connections between the various modules in your project.
The Project Modular Area can contain as many modules (Racks, MUXes, VST plug-ins, etc...) as you want and each sub-MUX also is completely modular.
You can go as deep as you want. You can see it as a tree with the Project Modular Area being the root. The Project Modular Area is a kind of MUX itself, but slightly different.
In stand-alone apps like MuLab, the Project Modular Area audio inputs receive audio from the audio device, its audio outputs send audio to the audio device and its event outputs send MIDI to the enabled MIDI output ports. On project level MIDI input is handled automatically i.e. it is send to the focused target module, cfr Focused Module Keyboard.
In plug-in apps like MUX Modular Plug-In, each instance of the plug-in runs in its own project, with each instance project having its own Project Modular Area.
That plug-in's Project Modular Area has a fixed number of audio inputs and outputs which connect the plug-in to the host.
More in detail: In MUX Modular Plug-In the MUX you're dealing with is not the project modular area aka root MUX, but a standard MUX inserted in the plug-in instance project modular area.
The fact that MUX Modular Plug-In is about a standard MUX inserted in a (hidden) project modular area makes it easy and straightforward to load/save regular MUX presets, open/edit front panels etc.
In MUX Modular Plug-In you don't need to access the project modular area.
Here is a picture that shows the architecture of a mu-project:
All compositions, parts, sequences, racks, synth and effect modules, samples etc... are part of a mu-project.
You can work on multiple projects in parallel, and copy-paste and drag-drop parts and modules between them!