How to request a positive reference letter from my former PI who does not know me very well?
So, as suggested I'll try to expand a bit my comment. I will assume you did a good job in your work and that the reference you would receive from who actually supervised you will be strong.

In my opinion, you can ask for two recommendation letters. One from who actually supervised you, i.e. the Research Scientist.
The second, from the PI, as you feel this might help you. In the end, you formally worked for them, so it would also be strange not to have a letter from them.

I think they will gladly accept and can write a nice one even if they don't know you that well, but if you feel it's necessary you could suggest they consult with who actually followed your work, i.e. the Research Scientist, to have a better idea of your skills. I would mention this to the Research Scientist when you tell them about the letter, something like "I will also tell the PI to write one for me, but they might ask you some tip on what to write, if that's not a problem".

Good luck on the admission!