Node and (probably by extension) Electron infuriate me with their custom requirements.
Several Rust libraries also tend to default to a predefined set of certificates (which makes sense for libraries supposed to run on bare metal as there are no system certificates there, but that's not really a problem on most Linux installs). I make it a point to always use the native OS roots in the code I write, but unfortunately that's not universal.
Having to bind-mount certificates inside of docker containers is also always an annoyance I forget about until I see the first TLS errors in the logs, but that's by design and probably a good thing.