Welcome to the lions den
So you’re willing to get down into the blazing furnace or the lions den and change the upload path. This is so not a good idea without investigating what is happening behind the scenes. I can’t give you a full write up, as there’s so much involved, like filters, options calls, constants, etc. but I can give you one recommendation: Don’t. Do. This. Things like that tend to work for a while. And then suddenly break, as you hit one of the edge cases. And you’ll be left wondering what happened. Callbacks, options, etc. will hide the problem from you and you will spend ages to trace this bug down.
EDIT
Don’t hand/hard code such stuff.
// Get original value
$temp = get_option( 'upload_path' );
// Assign custom value
update_option( 'upload_path', "wp-content/uploads/attachments/{$id}" );
// do custom stuff
// Move old value back in
update_option( 'upload_path', $temp );
The wp_unique_filename( $dir, $filename, $unique_filename_callback = null ) function takes three arguments. The third is a custom callback and optional. It takes three arguments: $dir, $name, $ext. Just use this one if you need to do this custom.
$dir– The first argument from thewp_unique_filename()fn$ext– retrieved viapathinfo()(PHP default fn) – the file extension. In your caseif ( 'pdf' === strtolower( $ext ) ).$name– The filename without extension
The custom callback can also be completely disabled (I don’t know what then happens – maybe the sky falls on your head?). You can do this by simply using the core functions of __return_false, __return_null (or maybe even __return_zero?).