Yes, you can.
For example, you have a CP that changes your default cat or dog you can also have extra skins with Alternative Textures. Or if you use one to change your farm for the farmhouse and want to use AT on the other buildings or even other farms.
The one thing that might have some conflict is using two different CPs for the same thing (ie: two different horse replacers) but AT can be used safely with CP in this case.