Disclaimer: My answers are based on Helm 3. So let's get to it:

• #1: No, in your values.yaml you define the static/default values. It's not the best approach to let static values in your template files (like deployment.yaml). To override the values of values.yaml The best practice is to use --set KEY=VALUE file. In this case, is totally possible to get the environment variable.
• #2: Can you give an example? Yes, sure.

For example, I want to install Elasticsearch on my cluster using helm so I use the command:

helm install elastic/elasticsearch --version 7.8.0

But I do not want to use the default values of the chart. So I went to https://hub.helm.sh/charts/elastic/elasticsearch and https://github.com/elastic/helm-charts/blob/7.8/elasticsearch/values.yaml, saw what's possible to change, then I create the command:

helm install elastic/elasticsearch --set minimumMasterNodes=1 --set protocol=https  --version 7.8.0

But in my CD tool, the minimum master nodes are different values and since this is an environment variable I changed my command line to this:

helm install elastic/elasticsearch --set minimumMasterNodes=$MIN_MASTER_NODES --set protocol=https  --version 7.8.0

So, as a result, the command above will run with no problem in your CD tool once the MIN_MASTER_NODES environment variable is provided correctly.

Your use of values.yaml to define environment vars is totally up to you. Is the value static? I'd have no problem leaving it in the deployment yaml. If it's a secret you should manage it either with k8s secrets or input it when you use helm install --set-value.. If the value is dynamic and is changed often or could be changed in the future that is the true use for values.yaml imo