Thanks for the responses everyone.
We commit the entire folder similar to what Ben’s mentioned - we don’t use Roots specifically but I follow a similar idea for it. I think having either the plugins + core themselves, or a reference to the version for each (so something like composer can install them all) gives a lot more control to make sure nothings out of whack between dev/staging/prod versions, and you know what is where.
We also have various htaccess rules, deploy scripts (we currently do deployment locally using PHPloy, readme/dev log files, special configs etc. If we just have the theme committed, then to rebuild a site would take a lot of manual work, which means we could have some errors between what you installed and what you were supposed to have. I think this setup gives us the potential to move to something like Bitbucket pipelines or Github actions in future - would be able to run node build tools for the custom theme, and composer for core/plugins and deploy all code in one hit. Our host is just a local cpanel/apache provider, so nothing special on their front.
Regarding the repo names, on Bitbucket they’re named correctly, its just that Gitkraken seems to prefer the folder name over the repo name. I know way back when I used Github Desktop for Windows I think it used to prefer the repo name, so might be a limitation of Gitkraken.