If I had to guess, Bowen might not be moved to the starting lineup at all, but his minutes will increase should they meet LA in the WCF.
Like it or not, Bowen isn't capable of guarding Kobe effectively for 40 MPG like he could in 2003, you're probably getting effective defense on Kobe from him for 25-30 minutes on a good day.
Although not the same situation, this is similar to the finals last year when Pierce was clearly the best Kobe defender on Boston, but could only guard Kobe for so long before losing too much energy. Because of this, they put Ray Allen on Kobe for most of the 1st quarter knowing Kobe would go off but knowing his offense would peak early on and Pierce could shut him down in the 2nd half.
In he WCF last year, SA blew a big lead in game 1 because Kobe got better as the game went on. LA blew game 2 open because Kobe got hot in the 2nd half. My guess is Pop noticed this and that's why Bowen won't be defending Kobe early on.