Yes, your structure will work. You can actually create master page on the Channel 1 and Channel 2 level, so each sub site will use it's own master page.
For shared content, you can use Linked Page option to virtually show a page from C1 under C2. And if the template setting for that page is set to inherit from parent, when C1 page displayed in C2, it will have the C2 look and feel.
The permission would be the easy part as they are set on the folder/branch level.