Thanks for the positive feedback and for your question. I can give you a few suggestions for your application.
MLA does hook the wp_handle_upload_prefilter but does nothing unless the MLA-specific mla_upload_prefilter is also defined. If you haven’t defined the MLA filter you can use the WordPress filter however you like. You can also use the WordPress wp_handle_upload filter in the same way. The MLA filter is used in two “Mapping Hooks Example” plugins.
I also found another WordPress filter in the /wp-admin/includes/file.php file you can consider:
/**
* Filters whether to short-circuit moving the uploaded file after passing all checks.
*
* If a non-null value is passed to the filter, moving the file and any related error
* reporting will be completely skipped.
*
* @since 4.9.0
*
* @param string $move_new_file If null (default) move the file after the upload.
* @param string $file An array of data for a single file.
* @param string $new_file Filename of the newly-uploaded file.
* @param string $type File type.
*/
$move_new_file = apply_filters( 'pre_move_uploaded_file', null, $file, $new_file, $type );
I haven’t done any testing of my own, but any of the WordPress filters should work for your application without any interference from MLA. I am marking this topic resolved, but please update it if you have any problems or further questions regarding the above suggestions. Thanks for your interest in the plugin.