I would love to have a gadget that would allow me to place a signal inverter on any one of the colors of the incoming bundle

Bundled NOT:

The physical gate would have 1 bundled input, and up to 3 bundled outputs, cycleable like other gates, with any combination of outputs enabled/disabled

Once the gate is placed, players can access a gui. This will show the 16 colors as check boxes. When a player checks that particular color - it's output will be inverted.

Bundled AND:

The physical gate would have 1 bundled input, and 3 single outputs, cycleable like other gates, with any combination of outputs enabled/disabled

This would have a GUI that would allow you to enable or disable which of the inputs you use in the output test - enabling the testing of each color of the bundle or not.

These two gates would allow for very specific state checking in ProjectRed circuits.

I don't think there's enough need for gates like this. If you want to invert a few signals, just place down some not/buffer gates