Fitter suggested too short a stem
Assuming the fitter correctly positioned the saddle set back for you, moving the saddle forward could result in more knee stress and the potential for repetitive stress injury.  Keep an eye for early signs.  Your knees, hips and IT bands could all show signs. 

Typically, the recommended order of operation in the fit is to first set the saddle height and setback, then set the handlebar reach. Saddle position is considered one of the most important positions for overall performance.

I find it interesting that the more shorter reach setup relieved back pain. Usually a stretched out position affects the shoulders and neck. You should also look into if you have back and hip flexibility issues.  Fit can accommodate flexibility issues, but shouldn't be a substitute for addressing the underlying issues as they likely affect other aspects of one's life.   

This is rampant speculation (take with a grain of salt), but do you sit a lot?  If you slouch a lot while sitting you may have impacted your back and hip flexibility, giving you a more rounded back riding position and a shorter reach.

As a final aside if you carry a load on the bike, shifting the pacement of the load ahead of the handle bars can return some of the handling characteristics.