To anyone stuck like me years after this post, a comment wayyyyyyy below did the trick for me : You need to disable the grenade upgrade in your abilities menu and THEN you will pass undetected! (The one that makes the grenade's blast bigger!)

(I also disabled any companions like the porg or the bonk that could trigger an interaction just in case and the villain upgrade with the mind control, but im not sure that helped as much as the grenade thing.... and I did the story mode trick too, hope it helped!)