I haven't personally noticed any differences, but is there a toll on normal usage of iTunes and syncing it with your iPhone if you fit a developer profile by having Xcode on your system including relevant mobile components (Mobile Device Framework) that ask to be installed? I'm curious because during installation, iTunes is asked to be closed. I'm not part of the Developer Program yet and as such my phone is not yet marked as a development device.
The short answer is no, it shouldn't.
It asks to quit iTunes because Xcode needs to install its own 'hook' to interact with iTunes. Quitting iTunes just reduces any risk as it gets installed. For example, one of the iTunes plist may be getting updated during install.
As with Jeff's answer, backups may take slightly longer because there may be more data on there, but I haven't even noticed this myself.