Adding a suppressor changes the entire vibration characteristics of the barrel.
Also in my experience, I see pressure signs much sooner when shooting with the suppressor. Therefore if I plan to use the suppressor the majority of the time, I will work up a load with the suppressor.
I work up my loads unsurpressed, and once I get the load, I like to chrony it with the suppressor to see the difference, then rezero the scope. I use AAC and they actually have very little affect on FPS in my experiance, usually 50-100fps more.