I'veI had initially tried deploying WP to heroku with a port to use MySQL of Mhoofman's repo. The problem I ran into there was that the WP Read Only extension was breaking things like the importer and thumbnails, and it seems like it's not really under development anymore. That would otherwise be my preferred solution.
My latest attempt has been trying out Efeqdev's method setting up wordpress as a submodule. After running into issues serving static files in MAMP on OS X, I finally got it working.
Of course, once I did all the work and reading through the comments on post, it seems like the they had moved onto deploying using Bedrock. My hesitation about using Bedrock is that it seems like Composer will manage the plugins for me and might wipe out any customizations I may have made to them. As I said, not extremely familiar with PHP/Wordpress, so if I'm wrong about that, and it seems like a saner option, please do let me know.
It seems like moving around parts of WP has a lot of potential for things to break. Would it make more sense to keep the wp-content subdirectory in a git submodule and everything else in a standard way? Not entirely sure how to deal with stuff in the uploads folder, not a good idea to keep it in git, it gets modified in the server when new images are uploaded, and we're using cloudflare for media distribution.