Unable to uninstall with custom WiX installer - wpf

Question

I've created a custom WiX Burn installer using ManagedBootstrapperApplicationHost with a WPF frontend (using WiX 3.9).
The installation of my MSI works correctly. I use mBootstrapperApplication.Engine.Detect(); to determine if the MSI package is present or not. If it is, I follow a flow similar to that of the installation, in order to uninstall:
mBootstrapperApplication.Engine.Plan(LaunchAction.Uninstall);
Once it's in the PlanComplete event and the Status == 0, I call mBootstrapperApplication.Engine.Apply(System.IntPtr.Zero); and will eventually get back to the ApplyComplete event with Status == 0.
Unfortunately though, nothing seems to have happened at that point.
I'm hooked up to the ExecuteMsiMessage and it has no messages coming through. When ExecuteBeginis fired, PackageCount is 0, where I believe it should be 1.
I can post code if necessary. My wxs file looks like this:
<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi" xmlns:util="http://schemas.microsoft.com/wix/UtilExtension" xmlns:bal="http://schemas.microsoft.com/wix/BalExtension" xmlns:netfx="http://schemas.microsoft.com/wix/NetFxExtension">
<Bundle Name="CustomInstallBootstrapper" Version="1.0.0.0" Manufacturer="Square Enix Ltd." UpgradeCode="33CA185D-083B-4D45-A0AE-693C2E09C5F0">
<BootstrapperApplicationRef Id="ManagedBootstrapperApplicationHost">
<Payload SourceFile="D:\Project\CustomInstallBootstrapper\BootstrapperCore.config"/>
<Payload SourceFile="D:\Project\CustomInstallBootstrapper\CustomInstallBootstrapper.dll"/>
</BootstrapperApplicationRef>
<WixVariable Id="WixMbaPrereqPackageId" Value="ignore" />
<WixVariable Id="WixMbaPrereqLicenseUrl" Value="ignore" />
<Chain>
<PackageGroupRef Id="NetFx451Redist"/>
<MsiPackage Id="LauncherMSI" SourceFile="D:\Project\Launcher.msi" Cache="yes" Visible="no">
</MsiPackage>
</Chain>
</Bundle>
</Wix>
If I run the MSI on its own, I can install and uninstall it without any issues.