using drush site-install, administrator account doesn't get Panelizer permissions granted

When using drush site-install commons to perform a fresh install of Commons 7.x-3.x-dev, the administrator account gets all permissions granted to it except ~25 permissions under the Panelizer section:

Node Answer: Administer Panelizer default panels, allowed content and settings.
Node Event: Administer Panelizer default panels, allowed content and settings.
…
Node Wiki: Administer Panelizer content

The issue does not appear when I install interactively through the site.

I've been using a more complicated drush site-install command, but for troubleshooting purposes I've simplified it down to the following, while still being able to recreate the issue:

sudo -u www-data drush site-install commons \
  --db-url=mysql://commons_dev:commons_dev@localhost/commons_dev \
  -y \
  --account-name=admin \
  --account-pass=admin \

p.s. - I initially reported this in #1814284: Select all permissions for Admin role (comment #5), but now that I've narrowed it down to drush site-install, it seems to warrant its own ticket.