1) Yes, it works as design. Please, check documentation:
Miniconda is initially installed with a base environment containing a few packages needed for its operation. However it is not recommended to install programs in the base environment. Therefore, it is recommended that you create separate environments to keep programs isolated from each other.
<When you update your Miniconda version> Previously existing environments are not effected by the update. The update only makes changes to the packages in the base environment.
2) Due to License agreement with IBM Python 3.9.5 in a form of conda package is available only for customers on support for Rocket Open AppDev for Z. Unless you are a Rocket customer, you can't install Python 3.9.5 into other environments.
3) You can try to install boto3 from an open Anaconda channel (e.g., conda-forge) or using pip. Since it is a pure python package, I don't anticipate any installation issues. However, even pure python packages might require z-specific changes and we can't guarantee that packages installed from resources other than Rocket channels are operational.
Pip is a part of Python package and will be updated with it later.