I like this idea-- the pay-off should be that it was Dukoo posing as Qui Gon. At least that's a mystery with some intrigue for the audience and maybe we could be left to put it together ourselves that Dukoo was using his apprentice's name. It would add interest to the Obi Wan/Dukoo meeting.

If no fancy footwork can make Obi Wan say "Master Jinn was killed nearly ten years ago" then that line can be cut-- Obi Wan's surprise could easily keep him from interjecting that rather unnecessary info anyway.

Sy-dious made sense to me since it really is Sidious' plan. I imagined that, as a Sith, he could pose convincingly as a Jedi. But throwing Qui Gonn's name in here is more visceral. It makes the stakes feel personal for Obi Wan. He has to get to the bottom of this for personal reasons as well as for the council.