If you are talking about changing settings in your display modes, those are global options, so you will not be able to set them on a per-model basis, sorry.
Probably the easiest is to modify your display mode as you want and save it under a new name. Continue to modify your mode(s) and save each version that you like under new names until you have all the different customized modes you want - there is no limit. Then all of those modes will be available in all of your Rhino files, you just have to choose the one you want for a particular model.
@pascal
I’m just hitting this issue now. I have 8 instances open. Right now if I tick the flat shading box in my Shaded mode, all of my other instances now go to flat shading in the Shaded mode. Same applies to all other settings in the display tab. This is a huge inconvenience. Flat shading demands significant resources on complex models especially high res meshes. There are some cases where I can’t even navigate the layouts of a model if flat shading is on.
Please tell me this is a bug and about to be fixed soon.