To expand on Tom's answer, if you remove the Disables from your Bundle tag
<Bundle Name="$(var.ProductName)" Version="!(bind.packageVersion.MSIPackage)"
Manufacturer="$(var.ProductManufacturer)" UpgradeCode="$(var.UpgradeCode)">
You can modify your MsiPackage tag to hide the MSI from Add/Remove Programs
<MsiPackage
Id="YOUR-ID"
Vital="yes"
DisplayName="$(var.ProductName)"
SourceFile="$(var.Source.TargetPath)">
<MsiProperty Name="ARPSYSTEMCOMPONENT" Value="1"/>
</MsiPackage>
This will leave just one entry in Add/Remove Programs. Your Bundle will now handle the UI of the install and uninstall, and will correctly allow other versions of the bundle to be installed.