To fix this problem you can set up you CI server to merge into the base branch automatically before running the code (in fact you should probably do this by default for other reasons).
This way your devs won't have to merge, they can just rerun their tests, which should be the same workflow as if your CI config is separate from your codebase.
I've been using GitHub actions for my personal projects for the past few months. The documentation was not the best and the UX was not polished at all, so the experience was painful sometimes. A lot of my problems will be solved with the features announced today, except I'm not sure if they're also adding a way to cache e.g. dependencies between jobs.
While writing your own actions was painful (at least for me), reusing actions that other people wrote worked like magic. I think the reusability aspect is going to be huge when Actions get more and more popular.
This way your devs won't have to merge, they can just rerun their tests, which should be the same workflow as if your CI config is separate from your codebase.