I was able to solve this after finding a thread on Wix User's mailing list. Here it is:
customizing burn prerequisite boostrapper image in theme
So this screen is known as Burn Prerequisite and it has a special WixVariable ID. Here is code from my Bootstrapper, depicting the use of my own custom theme for Burn's pre-req screen:
<WixVariable Id="PreqbaThemeXml" Value="..\resources\MbaPrereqTheme.xml" />
<WixVariable Id="PreqbaThemeWxl" Value="..\resources\MbaPrereqTheme.wxl" />
And any resources like Logo.png, Banner.bmp and NetfxLicense.rtf etc which you have referenced in MbaPrereqTheme.xml, would have to be part of Bootstrapper as a PayLoad:
<BootstrapperApplicationRef Id="ManagedBootstrapperApplicationHost" >
<Payload SourceFile="$(var.BootstrapConfigFile)"/>
<Payload SourceFile="$(var.MyBootstrapDll)"/>
<Payload SourceFile="$(env.WIX)\SDK\Microsoft.Deployment.WindowsInstaller.dll"/>
<!-- Following are required as payload and to be used by Pre-Req screen.-->
<Payload SourceFile="..\resources\logo.png"/>
<Payload SourceFile="..\resources\Banner.bmp"/>
<Payload SourceFile="..\resources\NetfxLicense.rtf"/>
</BootstrapperApplicationRef>
And this started working just like as I wished :).
Regards