Thanks for your work on the APK diffing! I had to fix a typo to get it running that was introduced in diffoscope commit fe7ae15e1c177866acd478af4cc4a51bd5002017 at the bottom of it. It turned 'f_out' into a non-existent 'w'.
With that change, diffoscope is now working for me again. I'm running it on the fdroid verification server, you can see the output here: https://verification.f-droid.org/ Also, about apktool.yml, I don't think we need it at all in diffoscope. It is not a file from the APK and it is not produced by Android SDK tools. As far as I know, it is only used by apktool if you want to use apktool to reconstruct a previously "decoded" APK.