Wow, great work getting it going! The bundled ~/.indigo/ssl/ca-certificates/cert.pem
is originally provided to Indigo by Homebrew. That's because we run a build server which builds Indigo's services from Homebrew's, with the build scripts modified as needed to allow them to run completely standalone, independently from Homebrew. To be clear, you don't need Homebrew installed, and if you do install it, Indigo won't be affected, nor will it affect, your Homebrew install.
I'm sorry that I'm still at a bit of a loss understanding why the bundled certs are not working for you. I do some pretty complex inter-server communication stuff using my Indigo stacks (albeit using Guzzle not curl) so I can vouch that "it works for me" — for what that's worth ha! Given that you succeeded in getting it working, are you happy to leave the debugging there and move onwards?