For claude at least I have been getting more assumption clarification questions after adding some custom prompts. It is still making some assumptions but asking some questions makes me feel more in control of the progress.

In terms of the behavior, technically it doesn’t override, but instead think of it as a nudge. Both system prompt and your custom prompt participates in the attention process, so the output tokens get some influence from both. Not equally but to some varying degree and chance

Not for me, at least with CharGPT. I am slowly moving to Gemini due to ChatGPT uptime issues. I will try it with Gemini too.

It does. Just put it in the custom instructions section.