No, a tuner is not going to change the tune because you have a different setup from the cat back. Most tuners are assuming that if you went though the trouble/expense of installing a 3 inch DP, that you will also change the entire exhaust. But its the dp that makes the most dif.
Listen to Drew, like he stated most tunes/tuners just ripped the others off, sorry, copied, and maybe changed something here or there. The best tunes are the road tunes, one where you live close to a tuner that has this capability, or do it yourself. You can also get a mailbox tune, then put it on a dyno, plot all the a/f ratios, etc then you send that info along with the ecu back to the tuner where he makes adjustments.