Obviously, my solution was very easy and could be detected by myself when trying to reboot after MSI install:
When telling the MSI package to reboot after successful install by applying
<InstallExecuteSequence>
<ScheduleReboot After="InstallFinalize"/>
</InstallExecuteSequence>
to my wxs file of my MSI project it will not cause the MSI to restart after the setup in the setup chain. Instead of that it will give the bootstrapper any return code so it enables my reboot text and button on the end of the whole setup chain.
I did not expect the bootstrapper is so intelligent. Nice!