Chado is patched to adapt to Debian file system hierarchy, using quilt.
For more info on quilt, see /usr/share/doc/quilt/README.source.

Regarding lintian warnings:
W: libchado-perl: maintainer-script-ignores-errors postinst
  Errors are not ignored, errors are catched in the script as some error codes are a correct behaviour in scripts.
  Other error codes are thrown as usual

W: libchado-perl: package-contains-upstream-install-documentation usr/share/doc/libchado-perl/INSTALL.Chado.gz
 Lintian override:
 INSTALL doc is required for database optimization setup and manual schema installation if automatic setup was not used.

Binaries tools are not set in /usr/bin but under /usr/share/gmod/chado/bin because part of those scripts are used by other gmod tools, not necessarly with same version and not necessarly all same tools, leading to conflicts.