The way our installers currently use conda results in all of the conda packages we install going into the base environment. That goes against the recommendations of the Anaconda team (https://conda.io/docs/user-guide/getting-started.html#managing-environments), as it makes it difficult to create completely independent environments using the same conda binary.
It might of course be best to have different conda binaries for different environments, but it appears this is really not the way conda wants to work; it wants to have one conda tool for all environments, and regularly puts stuff I'd consider environment-specific into dotfiles in $HOME. It might be possible to prevent that by being careful with command-line arguments when we install miniconda; having our conda install not do anything global would be another way to address this issue.
I am going to try to just install a separate miniconda as a workaround for this, as I'm sure many other LSST users have done successfully before, but the presence of shared content in $HOME still worries me.