In terms of implementation, one key difference is that Cloudflare sits between your servers and your users, whereas with Gatekeeper, your servers query Gatekeeper before deciding what response to send to users. One of the ramifications is that with Gatekeeper, your users never see a third-party page about verifying that they are not bots. It also means that when using Gatekeeper, you can actually debug if/when something unexpected happens.
Gatekeeper also allows you to look over previous traffic patterns and adjust your custom rules. Philosophically, our assumption is that website operators know their sites the best, and know what content they are sensitive about and Gatekeeper is a tool to help review traffic and express custom rules. I think Cloudflare is a better fit for operators who don't want to spend time fiddling with various very granular knobs to optimize for their specific site and their specific concerns.
Gatekeeper can also be used for other purposes. For example, the idea behind Gatekeeper originated because we have a site where we want to make information freely available to humans, but not to scrapers. However, Gatekeeper could also be used to upsell users who frequent your site (e.g. "We noticed you've viewed 10 articles in the past week, please subscribe!").
If you're considering custom logic like https://news.ycombinator.com/item?id=33160679 , Gatekeeper already has a rules engine so that you specify such policies without having to write your own infrastructure.
I'd be happy to chat further to learn more about what you're looking for and to see if Gatekeeper might be able to help. Feel free to reach out via email (in profile) if you'd like to talk more.