I have a custom BA which requires .NET. This is included in the chain as a PackageGroupRef to be installed before anything is done.
The approach followed is defined in this blog: http://blogs.msdn.com/b/heaths/archive/2011/10/28/introducing-managed-bootstrapper-applications.aspx
The only difference is that instead of DownloadUrl, I use a SourceFile so that the user does not need to download .NET.
Cancelling the .NET installation and restarting the custom BA seems to have issues.
Steps to reproduce:
1. Start the custom BA without .NET
2. Accept the .NET installation but cancel it before it completes
3. Restart the custom BA
4. Accept the .NET installation and do not cancel
5. The .NET installation says it failed
However the .NET installation was successful and starting the custom BA now starts it without the popup for .NET and goes to the welcome screen.
I just tested this with WiX 3.7 on XP 64-bit and .NET 4 Full. At step 5, my custom BA successfully launched without any error messages.
Burn creates very good logs. You might want to create a bug at http://wixtoolset.org/issues/ and attach them.