We are glad you like the work we have been putting into our Colorization! You should be happy to know that we currently are working through most of your suggestions! Yes, the Site Color tool will be your best bet for now if you want to place color in the rest of your plan. Take a look at the documentation showing how to do this.
You can place it within an area that has already been hatched with a RefNote, but you need to be very careful not to replace the hatch with the color. So, if you are prompted to replace the Land F/X data to an area, just say no and you should be safe.
You can absolutely assign a concept plant a color symbol. When using the Colorization tool to turn on your colors, simply look for the Concept group name and assign the symbol there.
Lastly, the linetypes is another one we are playing with and building out a bit more. If you have any examples you would like to see implemented please send us a tech support ticket with your examples and we can take a look at them.