Is there a way to capture uncommited changes with 

Task.create

 just like 

Task.init

 does? Actually, I would like to populate the repo, branch and packages automatically...

You can pass a local repo path to Task create I "think" it will also store the uncommitted changes.

I start my main task like this: 

python my_script.py --myarg "myargs"

. How are the arguments captured?

At runtime when argparse is called.
You can use clearml-task CLI to take an existing code and create a Task from it:
https://clear.ml/docs/latest/docs/apps/clearml_task
https://github.com/allegroai/clearml/blob/master/docs/clearml-task.md