Hi @prhodes
There are a few posts around on this topic (such as Netlify function works with ntl dev, but returns 500 after ntl build, and https://answers.netlify.com/t/can-netlify-functions-be-manually-deployed/37442) all seem to not have solutions. So I have run a little test.
I created a GitHub repo (https://github.com/coelmay/netlify-github-functions) with the basic hello function from Netlify Playground which I deployed to https://coel-functions-001.netlify.app/.
I then created an exact copy of this and deployed it to Netlify via netlify-cli to https://coel-functions-002.netlify.app/.
Both versions where tested with netlify dev and both worked. However, when I deployed them the GitHub version works, but the netlify-cli version returns a 500 Error.
I generally only use netlify-cli once I have a site deployed via git first, so perhaps I have done something out of sequence.
Perhaps @perry or @luke (or others) might have something they can add, or find error in our methods.