I might write my own CLI tool to publish apps, rust has good libs for apk parsing which seems to be the main issue I'm having

What's blocking you?

If you want to go down that path we could eventually embed the APK parser in the Dart app? Otherwise I want to help you. Other devs have definitely been able to publish from Linux. Apktool is a Java jar that has to work everywhere. Are you running Ubuntu? I will try to reproduce and fix all I can