Hey @snr - thanks for the bump. I work on our Local engineering team and was chatting about this with Nick and a couple of our engineers this morning.
What you’re describing is “expected” in the sense that Local doesn’t support Bedrock out of the box. That doesn’t mean it isn’t possible to get there, but as you said, the users who have figured it out are using some hacky workarounds.
Shell Script
You’re correct, that script is auto-generated each time the “Open Site Shell” button is clicked. The best option here is to edit the script as you have done, create an alias for running the script that you can call from a plain terminal, and then don’t click that button again. Clicking it would result in overwriting the changes.
SSL
You’ll want to restart your site for any changes to the .hbs files to be registered; this will regenerate the site with the changes.
An option for getting it working would be to provide the full path to the certificates that ship with WordPress - this would be the full path to /wp-includes/certificates/ca-bundle.crt.
For a more complete “better Bedrock support for Local” discussion, I created a feature request on the community forums - Support Bedrock in Local. This will allow others to upvote and jump in on ways we can improve this workflow.