quick question about overrides vs Image Handler2 addon

[DrByte]

IH2 wants to replace the following:
\includes\functions\html_output.php
\includes\modules\pages\popup_image\header_php.php
\includes\modules\pages\popup_image_additional\header_php.php

is there a way to override those instead of replacing them?

No, there are no overrides for those files. You'll need to replace them.

I also see that it wants to put this:
\includes\templates\template_default\jscript

into the template_default folder. shouldnt that be in:

includes\templates\my_template\jscript?

Either way is fine.