Also, I should mention that I build the Android app with android:debuggable=true in the Manifest.
On and Android device, that is what should trigger CheckJNI to be enabled.
Not so on Chromebook Chrome OS ARC.

This is tricky since it needs to be enabled before an app launches, but to issue adb commands you generally have started an app in ARC.

One option might be to override the default shell command that launches the activity.  You can maybe inject an "adb shell setprop debug.checkjni 1" before the launch.  For instance, in metadata:

"shell": ["setprop", "debug.checkjni", "1", ";", "am", "start", "$launch", "--activity-reset-task-if-needed", ";"]

This is untested and may require a bit of munging to get to run correctly.  This has never been used in ARC before either so it's possible not all the CheckJNI functionality works.

I'll give it a try.
But I see references to CheckJNI being used in some of the other issues listed when searching for "CheckJNI"
For instance  Issue 332079 
https://bugs.chromium.org/p/chromium/issues/detail?id=332079

Your suggested metadata didn't have an effect.  But I'm not sure I'm using it correctly.
At the bottom of ARC Welder, I can specify "Additional Metadata" and I'm assuming this is where you expect me to add your suggested JSON data.
The actual string I used was:

{"stderrLog":"V",
"shell": ["setprop", "debug.checkjni", "1", ";", "am", "start", "$launch", "--activity-reset-task-if-needed", ";"]}

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