Here is my proposed solution:

 1) add a config_ini.ini file to the jinja2 template. AFAIK it is the
    only one that needs it.
 2) the file consists of (not indented):

     [main]
     template_engine = jinja2

    so it looks like a part of a valid ini file.
 3) change admin.py:AdminTool::do_install() with the attached patch.
    This patch loads config_ini.ini from the template directory
    if it exists. It then adds the settings found except HOME
    to override config file settings like rdbms_backend.
    It then passes these overrides to the init.install module.
    then it deleted the config_ini.ini from the tracker home
    if it exists.

This seems to work for me and created a valid config.ini file.
Bern can you try the patch and add config_ini.ini to your jinja2
template directory with contents as above.