I spent some time trying to get my dotfiles working with git-crypt. I really tried. However, I kept having problems with it. Bad problems, like accidentally committing unencrypted files to my repo. Undoing that means purging and re-writing history, which is a major pain.
Some of these mistakes were my fault. I thought everything was working after a reimaging and restore from backup, but had failed to re-initialize git-crypt so it didn't know it was supposed to be encrypting or with what keys. However, some were not. One of the problems is that due to the transparent way git-crypt works, a git show will always show you the plaintext changes, so there is no obvious indicator that something isn't going to be encrypted as expected. Git-crypt added a check command because of user feedback, which let's you check to make sure a file is being encrypted on commit. I ran into at least one situation where I checked a file with git-crypt check, and it reported that it would be encrypted, and yet on checkin it was still committed in plain text.
There is just too much danger of accidentally exposing the sensitive files you are trying to keep encrypted for me to have any confidence in continuing to use git-crypt as a solution. Which is a real shame, because the transparency which is its weakness is also its biggest strength. I was able to easily add it into the dotfiles script to handle unencrypting automatically which made it frictionless in normal use, at least on the receiving/installing end of things.