I will start without the suppressor if there are any concerns over bullet stability. Long bullets, marginal twists, slow speeds (including subsonics), generally speaking things where there's a chance of finding a keyhole on the target. Or if there's a chance the bullet doesn't make it to the target, like how I'm trying to make a 223 Rem push a 30gn bullet through a 7 twist fast enough to go poof.
After that I develop with the can on. I figure I can sit there and turn a 6oz brake tuner half a turn and change the dispersion of a group, there's no way a 12+oz suppressor doesn't change the barrel tune. It might change it in a very consistent and repeatable way, but it will change it. So easier to do it with it on the first time.
I have an ATS tuner sitting on my shelf waiting for the day I either can't tune a load with the can on, or for some reason a suppressor makes my groups blow up. It's been waiting a while now

But maybe I don't see suppressors make groups worse because I work up with them and rarely/never shoot factory ammo in those rifles.