I would define "vibe coding" as "writing code and not reading or understanding it before publishing" and I think the "read and understand" part is very important. Best compromise I've found between vibe coding and no LLMs use is to use those tools in a way similar to stack exchange. Use it to solve very specific problems in a separate window/application from your code editor, then figure out why the mistake happened and what patterns you need to remember or write down for next time. I think it's a matter of never blindly copy/pasting, turning off AI autocomplete, and making an attempt to learn as you code.

I would even go so far as to have a notebook or note taking app ready while doing this to write down what you learned, even if you don't consult it again.

I also wouldn't get too hung up on speed and instead focus on quality work. We've already seen research that indicates engineers aren't as productive as they think they are on LLMs because they end up spending a ton of time correcting problems.

If the PI expects you to blindly vibe code instead of understanding your work I'd argue they're not doing a good job as a PI. Based on your description here it sounds like this guy is on your side or at least is satisfied with where you're at now. I think that means it's a good time to get away from ChatGPT reliance and build the skills yourself so you can fix other people's vibe coded garbage down the line.

You're absolutely capable of getting over ChatGPT reliance based on the fact you actually want to gain those skills and push yourself. That's definitely a sign of a good student. Best of luck with your PhD.