Not sure if I can answer your question. But I can tell you that I have many CA's in Basic MSI projects and they all work as you expect that they should... either when I execute the individual .exe's or when executed from a Suite. You mentioned that you use the msi file in your Suite. I use the .exe files.
I have tried both ways... I have exported my Basic projects as MSIs and EXEs... maybe my problem is that I am not exporting them the right way. How do you create your EXE files from your Basic project(s)?
If I understand your question... you want to know what options I have in the Setup.exe tab under Release for my Basic MSI projects???? Please Understand that I am not trying to tell you how to do it or that the way I did it is the most correct.... just sharing with you what I did and that seems to work.
Setup Launcher - Yes
Generate Package Definition File - No
Required Execution Level - Administrator
Advertise If Prerequisites Are Elevated - No
Include MSI Engine - Yes
Cache MSI Locally - No
Well, you see I have been passed the IS portion of my project from another developer. The other developer was using 2009 to build our last release for our product. We just upgraded 2012. I imported the all of the old 2009 projects into 2012 and was using the Project Assistant to select "Single EXE" to export the Project to be used in a Suite project. We had multiple Basic project to install each of our features. I have been given the task of bringing these into one installer. I see now that the original Basic MSI project are not building the EXE files correctly. I thought that maybe it was the way I was building the EXEs through the Project Assistant was causing the EXE to fail... I think maybe it's the transition from 2009 to 2012.