What operating system and tools should a beginner use to learn programming

Chances are you'll have to switch to whatever your job has eventually so just pick what you like. I really like VsCode personally because you can read the documentation of methods without leaving your program. The best system and tools is whatever gets you to start learning though.

I want start with python but I don't know what operating system and tools to use

Python is great and easy to learn but I think it leads to misunderstandings about how programming languages work if that's your only experience. If you can get a Programming Fund 1 class in C or C++, you can transfer over those skills to Python in a week. If you start with Python, then you'll be mostly starting from scratch if you need to learn other languages. But it's entirely your choice.

In terms of programming institutions (universities bootcamps, etc..), do each institutions have its own preference or does it let its student choose?

My university had Windows for the public computers but as long as you turned in your code it didn't matter where it was written. I know lots of people who used a Linux VM that they carried on a USB stick. They completed their assignments just fine.