How about not rewriting any of the folders. Have the module dump the drupal folders and files into the /web/ folder, and then just have a .htaccess file in the client's folder? Or maybe a standardized way of rewriting in the client's vhost file. If the client doesn't use the module for the install, then the client has to find some other way to get clean urls. If the client uses the module, then the module would just add a few lines to the vhost file.
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