Yes they have to be removed. PC has to be baked at I believe 400 degrees (I could be wrong) You can only PC metal, anything plastic, rubber, etc... will melt. Also if the tolerances are tight in the Cush Drive holes you need to tell the PC to tape it off, otherwise you will spend time sanding PC to get new cushes in. Most PCs will sanblast everything, you need to be specific on what to blast and what to coat. If your not specific they will F' it up. Or like in my case, you can say hey you f'ed up and I want a discount! In my case they blasted the motor mount holes on my frame, but didnt PC them I had them discount half the price of STM frame plugs. I havent pulled the Cush drives yet, Look in Syder's or Hayne's manual.
You will destroy the bearings getting them out. Just write down the numbers and either get them from Ducati (expensive) of a bearing shop like King Bearing(less expensive). Its just a normal SKF bearing. I had to use a punch and then pry them out, you can also apply some heat, not too hot!