Pentaho Data Integration CE is free and open source, and does ETL well. It's even "big data" friendly as it can transform it's code to run on Spark
There's a cookbook on Safari for it (free week trial):
https://www.safaribooksonline.com/library/view/pentaho-data-integration/9781783280674/
I don't have experience with Prefect but check this podcast featuring prefect creator if you haven't already -
I was searching for the MySQL ETL tool, and I must say that your top list is outdated. Here I found the detailed description of the top free and paid ETL tools for MySQL on the end of 2021.
Consider using Python w/ Pandas dataframes as an alternative to Excel - and you can automate the work with Airflow or some other scheduler.
Happy to jump on a Zoom to discuss if you'd like.
Two git repositories you mean? You could investigate using a 3rd super-repo that has the two repos as git submodules.
https://git-scm.com/book/en/v2/Git-Tools-Submodules
https://github.blog/2016-02-01-working-with-submodules/
You might need to add an extra step to get the submodules pulled/updated, not sure.