Xam Studio changes the build process if you haven't already learned from the release notes at http://developer.xamarin.com/releases/studio/xamarin.studio_5.9/xamarin.studio_5.9/
They removed the ability to create IPA files like we used to and essentially want us to remove AdHoc and AppStore configs and just have DEBUG and RELEASE like in Visual Studio typical development and "simplify" things. I don't think they should have done this, ADD the new workflow but don't remove what existed, there's nothing wrong with keeping the ability to have IPA builds done at build time. The new build process is actually broke for me as it is not detecting my signing certs which @jstedfast fixed today. I personally don't like this building an archive system as well as you have to have the signing just right for it to work (Release|iPhone) yet the menus remain enabled and just show you a fail message.
The WARNING I want to share is from a lesson learned today. In our AppStore and AdHoc configs WERE compiler constants. We have code flows based on DEBUG, RELEASE, ADHOC, APPSTORE. Because I cannot build an AdHoc or AppStore in 5.9 due to the signing bug I went to another Mac that has the previous STABLE set and pushed a build to my beta team. Sure enough developer "things" got exposed to the beta team which could have been bad. Caught it about 9 installs in and pulled it from HockeyApp (and Test Flight pending review).
So beware - before you nuc your AppStore and AdHoc builds DON'T FORGET your compiler constants and code ramifications. Now I'm considering adding more profiles such as I do in VS such as Distribution, etc. so what were we really trying to accomplish in this change? It's not ABNORMAL to have AdHoc and AppStore so let's not try to force people to remove it and at the same time let me build an IPA as before. The archive system "may" be nice for those that want to build multiple platforms at once but I don't think this was a good change and really complicates things such as continuous integration and maybe even our xamarin insights curl dSYM sending.
Major problems with the iOS 8.10 build as well, I'm not sure what happened to Xamarin in this release sequence - Q/A did not do a good job I'm sorry to say.