Ok, retested and found the cause We renamed the proguard.cfg to another name in our test and forgot to mention it in our answer. Sorry about that.
You were using proguard.cfg as filename. If the gradle plugin finds this file, then it will replace the whole internal Gradle configuration with it, even if you specify it as append in the build.gradle.
If you specify proguard.append.cfg, then it will be automatically appended, no need to specify it in the build.gradle.
So the solution is to remove the -keep class **, remove the appendCfgFile setting in build.gradle and rename your file to proguard.append.cfg. (or keep the appendCfgFile, but use a different filename - I tested with proguard-other.cfg)
The special behavior of proguard.cfg is documented here:
I opened an issue on GH, to add this special corner case to the documentation / Gradle plugin should throw an error in this case:
Thanks for the report.