From what i have seen from the docs and my experience so far
meteor run ios
only runs the iOS emulator with your code in it. The code related to this build is in .meteor/local/cordova-build but is temporary and will get overwritten all the time
meteor run ios-device -p yourlocalip:yourlocalport
will launch XCode with the cordova-built .xcodeproject, and a local server on your computer. It is intended to make you able to run and debug your code from an actual iPhone device, with the changes you make on your computer to the code repercuted instantly on the iPhone screen. You need your computer and your phone to be on the same Wifi to enable this feature. The code related to this build is in .meteor/local/cordova-build but is temporary and will get overwritten all the time
meteor build /Path/To/Builds/Directory/NewBuild -p yourserverhost:yourserverip
will actually create the cordova-built .xcodeproject pointing to your real server at the path you specified. From this project you can customize as much as you want BUT you will indeed loose these settings with a new build...
Except if you use the yourproject/cordova-build-override/ folder !
As described in the offical cordova meteor docs under "Advanced build configuration" everything you put in this folder will overwrite the files created by meteor during its build. So you can configure everything in the Cordova/Phonegap way there. If you were able to configure your features through Cordova usually, you will be able to do it there.
Bonus that I have learned the hard way :
Always destroy the .meteor/local folder before building one of those three things, i got stuck in a state where XCode remembered some of my changes to the .xcodeproject and everything was messed up. After destroying this folder, everything went back to normal :)
hope i helped
Mickael