This mean that the "installed product" detection algorithm of SilentBootstrapperApplication is inadequate in this case. I have created the issue from your report.
If you are still keen to use custom BA then you can take the WixBootstrapper_NoUI sample (an equivalent of SilentBootstrapperApplication). Though you will need to update the detection algorithm to make it suitable for your scenario.
If you are still keen to use custom BA then you can take the WixBootstrapper_NoUI sample (an equivalent of SilentBootstrapperApplication). Though you will need to update the detection algorithm to make it suitable for your scenario.