I still think the primary cause of the 'modifiers afterwards' line is because different spells face different negative modifiers, such as visibility modifiers, and they want those to apply to each spell separately. It's still a really messy rule though, and it doesn't help that Multiple Attacks in itself is a small disaster as far as I'm concerned. (Not that I blame the writers, but things went wrong there somewhat.) And now you get why it's in my list of controversies.