It can't get much simpler:

Drupal root URI is /
Gallery2 root URI /gallery2

Drupal root file path is .../html/
Gallery2 root file path is .../html/gallery2

My Gallery2 installation is configured for multi-site.

The "Gallery2 location settings" box at /admin/build/modules reads:

Overview of your Gallery2 location settings as specified or autodetected during install.
Gallery2 URL or URI: /gallery2/
Gallery2 filesystem path: gallery2/
Embed URI: /index.php?q=gallery
Gallery base: gallery

The notes at http://codex.gallery2.org/Integration:Drupal:Installation indicate that the G2 "URL Rewrite" plug-in should be enabled, but that plug-in is not compatible with G2 multi-site installation. Nothing in those notes suggests that this warning message indicates any good cause for the warning.