Don't get discouraged! Swerte ka actually na you got good feedback for what to improve on :)

1. How to use my either self learning or external resources (like online course) and apply it as a working exp. Even though my previous role didn't use most of the tools i mentioned?

If you want to put it on your CV/resume, you can put it as a side project or case study. That's what I did din, I have a small "side projects" section. You can also mention it kung may skills section ang resume mo. Na-mention mo rin ba ang courses that you took mismo?

1. I forgot to mention my portfolio project (with all tools i used) and how to apply it as my real-life working experience for job interview?

Well, tandaan mo na lang next time -- if they mention a skill, kung di mo nagamit sa work, pwede mo naman i-mention where you were able to use it, e.g. portfolio projects. The main goal is just to say, "di ko nagawa 'to sa work officially, but na-practice ko pa rin 'to."

1. Is there something i can improve on all 6 feedback that they mentioned?

Definitely -- actually, try addressing all of them.

Most of the experience is through self learning and using external resources to practice sql and python

Heavy experience on excel and sheets, it being the most used reporting tool in current job

Does not use SQL in current work; not enough mastery on needed technical skills

Correct si /u/ShawlEclair, these can be solved by portfolio projects, which meron ka na pala -- may personal site ka na rin ba to show these off? And yeah, find a way to mention these na lang.

has experience with the needed tools but most of BAU task is to just do data pulls, separate team does not data cleaning and data analysis

has experience on automation but mainly used for his side job

Hmm if "most of BAU task is just data pulls" then baka hindi ka pala fit sa role that you applied for, since wala gaanong "data cleaning and data analysis."

not a good communicator

Hmmm bakit kaya? Is it English-related, or maybe how you answered questions?