Hi,
1. What could be done in the future is to have an option in the custom file/ajax file fields to upload to another folder than the current one. But that's not really a problem. Another solution would be to have a "display template" option where you could have your own HTML with a tag for the file link. That way, even if the file would be in the secure folder, if the user seeing the field has access to the link, the link would work.
2. With what you have right now in the custom fields, the simplest would be to edit the view file displaying the custom field value and add some str_replace on the display function call of the custom field to change the current link to have instead a video tag.
So for example, for the display of the custom product fields on the product page, you would change the code:
<?php echo $this->fieldsClass->show($oneExtraField,$value); ?>
to something like that:
<?php echo str_replace(array('<a target="_blank" class="hikashop_custom_file_link" href="', '</a>'),array('<video width="320" height="240" controls><source type="video/mp4" src="', '</video>'),$this->fieldsClass->show($oneExtraField,$value)); ?>
in the view file show_block_custom_main.php via the menu Display>Views.