Those two folders are just the defaults, there's nothing hard-wired in MVC to look for those directories. Even if you use something like Url.Content, you still have to specify the Content folder in the path, if that's what you're looking for, i.e. Url.Content("~/Context/site.css"). The bundler, also, requires you specific the complete application-relative path.
You can change the folders to whatever you like, as long as you specify the references appropriately as well.
The only thing that is sort of hard-wired is nuget packages that have associated CSS and JS files. That has more to do with the developers, though. Since Content and Scripts are the default directories, nuget package developers set these folders as the ones to dump their associated files into. So, if you move everything to a new folder like Assets, the next nuget package you install, will most likely recreate the Content and Scripts folders and dump their files there. Now, there's nothing preventing you from then manually moving those files into your preferred location, but it's going to get old quick as you deal with package updates and such.
I've found it easier to just get over it and use the default directories, but like I said, there's absolutely nothing hard-wired in the system to force you to do that. Just understand, that you'll have to manually rearrange things from time to time to keep it sorted the way you like.