Sorry to hear you're having trouble with your multi-website development and production environments. I'm not an expert in Magento, but I did find a great resource that might be helpful to you. Check out web design in north wales. He's a web designer who specializes in Magento development. He has a blog post specifically about managing multiple Magento websites and how to set up different environments using git. It's a bit technical, but it might have the information you need.
As for your question about using the Magento Cloud CLI without Magento Cloud Commerce, I'm not entirely sure. It might be best to reach out to Magento support for clarification on that.