Can I remove the miniconda3 library?

Yes, you can remove the library.

Why miniconda3 is in /opt/ instead of ~/miniconda3/?

I don't know why, but the miniconda3 is in the /opt/miniconda3.

You may uninstall miniconda3 with the following commands:

1. cd /; rm -rf ~/.condarc ~/.conda ~/.continuum
2. cd opt
3. sudo rm -rf miniconda3
4. Open your bash or zsh rc file to remove miniconda from your path variable.

I used zsh, so I open -e ~/.zshrc to delete the context:

# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/Users/yilin/opt/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
else
    if [ -f "/Users/yilin/opt/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/Users/yilin/opt/anaconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/Users/yilin/opt/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda init <<<

In order to uninstall miniconda, simply remove the miniconda folder,

rm -r ~/miniconda/

As for avoiding conflicts between different Python environments, you can use virtual environments. In particular, with Miniconda, the following workflow could be used,

$ wget https://repo.continuum.io/miniconda/Miniconda3-3.7.0-Linux-x86_64.sh -O ~/miniconda.sh
$ bash miniconda
$ conda env remove --yes -n new_env    # remove the environement new_env if it exists (optional)
$ conda create --yes -n new_env pip numpy pandas scipy matplotlib scikit-learn nltk ipython-notebook seaborn python=2
$ activate new_env
$ # pip install modules if needed, run python scripts, etc
  # everything will be installed in the new_env
  # located in ~/miniconda/envs/new_env
$ deactivate