Even when trying to push files with CRLF ending, GitHub (or Git) normalizes them automatically. So when you download the raw script it always has LF ending. There is even this weird behavior that GitHub desktop on Windows gives a warning when changing the line ending in local editor to LF:
This is when I change it from CRLF to LF, and it changes it back. But what finally lands on GitHub always has correct LF ending regardless, even that the warning seems to indicate the opposite.
So if you run into such error again, please show in detail which command you were running/how you downloaded the script, and the exact error message.
Solution for the package overwrite error:
dpkg -P --force-depends gir1.2-gtk-3.0 libgtk-3-0 libgtk-3-common
apt -f install
Then rerun the upgrade script.