I noticed that WordPress is using the tmpfile() function which does not regard the upload_tmp_dir value. It would be better to use tempnam() instead.
these 3 files make use of the tmpfile function:
info.php wp-admin/includes/class-wp-filesystem-ftpext.php wp-includes/js/tinymce/plugins/spellchecker/classes/PSpellShell.php
I am a shared host and normally customers have their own tmp folder but tmpfile always writes to /tmp/ on *nix systems, so I have to give them more permissions than usual.