Include env defaults from `variables.properties.env` in deep merge

[kevingrismore]

The deep merge for env from the deployment->work pool only worked if the env vars were written directly into the template. This copies down the defaults to include them in the deep merge as well.

Checklist

• [ ] This pull request references any related issue by including "closes <link to issue>"
  • If no issue exists and your change is not a small fix, please create an issue first.
• [x] If this pull request adds new functionality, it includes unit tests that cover the changes
• [ ] If this pull request removes docs files, it includes redirect settings in mint.json.
• [ ] If this pull request adds functions or classes, it includes helpful docstrings.