Few problems we had with let's encrypt.Pretty neat was not aware they did this with commodo.
This works for the end user the same as the WHM let's encrypt plugin thou it's also ssl by default on all hosted sites for that WHM instance.
1. It needs to be renewed every 3 months. In some cases it would just fail. Why it would that we couldn't figure out. We the had to delete the certificate and issue it again. this happened to various domains, randomly.
2. We had 2 cases where the client had to buy a ssl certificate as the let's encrypt one was not accepted for pci compliance. Am sure this will change soon.