What is the difference between company routes and pilot routes?
A company route, or coroute, is just an easy way for the pilots to download the flight planned route into the FMC, without having to enter every route segment manually. It saves a bit of time, especially on longer routes, and eliminates the risk of input errors.

I haven't heard the term "pilot route" before, but presumably it just means the lack of a company route - i.e. a route that the pilots have entered manually.

Functionally, once the route has been entered in the FMC, there is no difference between a company route and a route entered manually. The only difference between the two is the way they are entered.