When attempting to use the ManagedBootstrapperApplicationHost, it wouldn't load assemblies with dots in the file name.
For example, Wix.Custom.UI.Test.dll would not work, but after much troubleshooting, discovered that WixCustomUITest.dll would.
Would also recommend that if the assembly isn't able to be loaded, the bootstrapper should provide better diagnostic information as to why. This was exceedingly difficult to troubleshoot and we only stumbled upon the problem by accident. Failure log attached.