I tried to create a subtemplate-comments-comment.php in /wp-content/themes/montezuma but the content was not picked up. Also I cannot see how the rendering is called, the comments.php seems not to render the comments, just the use-cases when there is a password protection / no comments.

I need to add a custom php function below each comment, how can I do this?

Thanks

I would add a dynamic widget to the MTO->Sub Template->comment.php->One Comment in Comment List option and then install teh 'exec php' plugin, add a text widget to your new widget area and then put your php in it.

Is there a way to actually replace the subcomment template with a file? I don't want to use the widgets hack and prefer the real files over the virtual template anyway. (which leads me back to wondering what file contains the call to the comment rendering itself)

If you don't want to use the virtual templates you are losing the big feature of the theme - with the virtual templates, during the next update you don't have to make the changes again. If you change a physical template and update it, you lose your changes.