Currently, the instructions for the staging environment mention not to use it for development environments, and instead suggest using Pebble. Staging Environment - Let's Encrypt - Free SSL/TLS Certificates
However, I don't think that this is a good solution to the problem in question. We want our development environment to match our production environment as closely as possible. Testing with Pebble does not seem useful with regards to that goal. If not for your rate limits, we would just use Let's Encrypt's production environment, but due to the nature of the kind of testing we have to do in this environment, that is not feasible.
I would like to propose that the staging environment be considered reasonably stable, and the only differences between it and the production environment be the lack of rate limits, and the use of a non-standard root. Let's Encrypt should also have an internal staging environment to test changes before they are released to the public staging and production environment, which would have helped prevent the issue that unfolded yesterday.