This would be a great assist to me; setting a distinct bundle identifier lets a built iPhone app install side-by-side with another build of the same project.

I concur. I'm currently trying to use a shell command prior to the Xcode plugin to set the CFBundleIdentifier value:
defaults write ${WORKSPACE}/Targetname-Info CFBundleIdentifier com.mycompany.mycompany

However, this results in a build error:

The following build commands failed:
ProcessInfoPlistFile /Users/Jenkins/workspace/MyApp/builds/MyApp.app/Info.plist Targetname-Info.plist
(1 failure)
Build step 'XCode' marked build as failure

I'm trying to figure out what is going on there, looks like something is messing up the file somehow.

Although I agree this issue functionality should be added, I'm currently using a pre-build script in order to change the bundle ID:

/usr/libexec/PlistBuddy -c "Set :CFBundleIdentifier $BUNDLE_ID" $PLIST_DIR/$PLIST_FILENAME

Esteban's code was merged in and will be available in the next release.

should be released by now.