I work on the official Python client for Let's Encrypt, but I support people's decision to use a different client if they prefer.
It's frustrating to see the occasional conspiracy theory suggesting that the Let's Encrypt project somehow wants to backdoor the client in order to compromise people's servers (an idea that occasionally gets brought up on our forums!). But it makes sense that some people want a client that doesn't modify their server configurations. The official client tries to modify server configurations because we believe that many people don't have the expertise or inclination to do it on their own. That goal does make the official client more complex, and there are still plenty of integration bugs to find and fix. If people want a simpler and more hands-off client without the integration features, they should definitely use one, and it's a valuable service that this option is available.