Instead of looking into the /ext/ directory for command extension, I would propose an alternative for the current plugin setup.
If you let the class CommandPluginExtension extend the Doku_Plugin class, you can load dt or template command extension by using the existing DokuWiki infrastructure for plugins:
example:
* one command extension per plugin*
This loads the helper component of the template plugin, if it exists.
$command_extension_template = plugin_load('helper','template')
this requires that folder structure of template plugin is:
[plugindir]/template/plugin.info.txt
[plugindir]/template/helper.php
* more commands extensions per plugin*
or if you want to provide more command per plugin.
Load the command extension with:
$command_extension_template_cmd1 = plugin_load('helper','template_firstcommand')
this requires the folder structure of template plugin is:
[plugindir]/template/plugin.info.txt
[plugindir]/template/helper/firstcommand.php
[plugindir]/template/helper/secondcommand.php
If you rename CommandPluginExtension to helper_plugin_command_extension, and you move it to [plugindir]/command/helper/extension.php. The autoloading of DokuWiki will load it when required.