The actual bootstrapper app is assembled in the project.OutDir. Usually it is a CurrentDirectory during the build (not 'bin/Debug'). Wix# compiler prints the location of the bootstrapper file in the output:
Windows Installer XML Toolset Linker version 3.10.0.2103
Copyright (c) Outercurve Foundation. All rights reserved.
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Bootstrapper file has been built: ...WixSharp.Samples\Wix# Samples\Bootstrapper\WixBootstrapper_UI\setup.exe
Name : My Product
Version : 1.0.0.0
UpgradeCode: {6f330b47-2577-43ad-9095-1861bb25889a}
bootstrapper.OutDir = "<your dir>"; //or bootstrapper.Build("<your dir>");