I misdiagnosed this -- the issue isn't that the flags aren't pushed to the device, it's that, when the device is rooted, they're pushed to /data/local/chrome-command-line, which the APK can't read.

The short-term fix here is the script counterpart to https://bugs.chromium.org/p/chromium/issues/detail?id=593720#c18 -- push to /data/local/tmp/ instead of /data/local/ in more scenarios on N.

Fix landed in https://codereview.chromium.org/2275863002/ and was manually rolled into chromium in https://codereview.chromium.org/2270313004

We're reverting this fix since it broke telemetry for some benchmarks on issue 641497. Anyway, I'll try to get this fixed soon as part of issue 593720.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/ac9c7854255ee68b7873d3dd31c2665b075de2d1

commit ac9c7854255ee68b7873d3dd31c2665b075de2d1
Author: catapult-deps-roller <catapult-deps-roller@chromium.org>
Date: Wed Aug 31 15:38:30 2016

Roll src/third_party/catapult/ fa2c4f219..aa7c58eb0 (2 commits).

https://chromium.googlesource.com/external/github.com/catapult-project/catapult.git/+log/fa2c4f21907f..aa7c58eb0459

$ git log fa2c4f219..aa7c58eb0 --date=short --no-merges --format='%ad %ae %s'
2016-08-31 perezju Revert of [devil] Use /data/local/tmp for the command line on eng + userdebug builds. (patchset #2 id:20001 of https://codereview.chromium.org/2275863002/ )
2016-08-31 nednguyen Fix flakes in csv_pivot_table_output_formatter_unittest.

BUG= 640228 ,641497

TBR=catapult-sheriff@chromium.org

Review-Url: https://codereview.chromium.org/2293973003
Cr-Commit-Position: refs/heads/master@{#415641}

[modify] https://crrev.com/ac9c7854255ee68b7873d3dd31c2665b075de2d1/DEPS

 Issue 652711  has been merged into this issue.

For some reason applying https://codereview.chromium.org/2275863002/ locally didn't work for me.
I managed to work around the command line issue by forcing /data/local/tmp in telemetry/telemetry/internal/backends/android_browser_backend_settings.py

After fixing the command line I am hitting the same issue with /data/local/chrome-trace-config.json

Benchmark runner fails with "Tracing is not started". 
I tried to redirect /data/local/chrome-trace-config.json to /data/local/tmp/chrome-trace-config.json in chrome and catapult but that is not working: chrome does not see /data/local/tmp/chrome-trace-config.json.

Juan, Ned, do you know if chrome-trace-config.json issue is being tracked and if there is a workaround?
If not I'll file a new issue.

I don't think this bug should be Pri=3 because it prevents us from testing on the newest Android.

The workaround is to ensure there are no chrome config files on *neither* /data/local/tmp/ nor /data/local/ before starting the test runner.

Also bumping up Pri.

Moving this over to catapult's issue tracker: https://github.com/catapult-project/catapult/issues/3112