Missing module warning for Kickstart themes, not resolved with standard fixes

Drupal throws warnings that commerce_kickstart_theme and commerce_kickstart_admin are missing from the file system, even on a fresh install of Commerce Kickstart. I'm seeing the warnings whenever I use drush to download contrib modules. The warning is thrown before the download even occurs. Example:

$ drush dl telephone
The following module is missing from the file system: <em                                          [warning]
class="placeholder">commerce_kickstart_theme</em>. For information about how to fix this, see <a
href="https://www.drupal.org/node/2487215">the documentation page</a>. bootstrap.inc:1138
Unknown path for commerce_kickstart_theme module.                                                  [warning]
The following module is missing from the file system: <em                                          [warning]
class="placeholder">commerce_kickstart_admin</em>. For information about how to fix this, see <a
href="https://www.drupal.org/node/2487215">the documentation page</a>. bootstrap.inc:1138
Unknown path for commerce_kickstart_admin module.                                                  [warning]
Install location .../sites/default/modules/contrib/telephone already exists. Do you want to overwrite it? (y/n): n
Skip installation of telephone to                                                                  [warning]
.../sites/default/modules/contrib/telephone.

I have tried the first two solutions proposed on the how-to-fix page linked to in the warning messages (https://www.drupal.org/node/2487215) without success:

1. The manual deletion via SQL works to remove the intended record in the database (as long as update the SQL to "type = 'theme'") but the deleted records immediately reappear as soon as you issue another "drush dl" command.
2. The "Module Missing Message Fixer" module does not see the offending records at all and gives a "No Missing Modules Found!!!" message.

This appears related to issue #2800333 "Missing module warnings on drush updb", but I'm creating a new issue because this is showing up in a newer version of Kickstart and because the message is appearing under different conditions.

It does not appear to be a critical problem for site functionality, but it is annoying and makes it hard to track and interpret command line output as you build a site using drush commands. Hopefully it's an easy fix.