I would be curious why this is a problem? Are there cases where you find ./ is not properly referencing the script?
The specific line in the export script is:
if int(args.url_type) == HypeURLType.ResourcesFolder:
url_info['url'] = "."
Using a "." here is a special value to indicate that resources should be placed alongside the .html file instead of in the typical .hyperesources folder.
As such, I think the only automated way to change this would be to manually parse and replace the text in the args.modify_staging_path section of the code.