Instead of writing a specific override to include main company in Projects, you can simply added main company to Customer group.
While it's not a very neat solution, it reflects the real procedure taking place.
Also - not every company would like to have their own company included there arbitrarily so we'll most likely leave it the way it works right now.
Of course you can modify the crits that are applied to this field - using your own, custom module (for crits callback) and simply updating field parameters (during module installation) is recommended (to simplify epesi updates in future).
Kind regards,
Arek