I've had to spend a lot of time messing with pre/post scripts combined with adding additional tools while converting over to PMP deployments. Sometimes it's resolving an incompatibility between exe/msi installers, sometimes there's other issues that make upgrades not go smoothly. To resolve this, I'll add a pre-script to run a cleanup utility from the manufacturer to remove all traces of the previous install before running the PMP deployment. I've recently had to make use of these cleanup utilities for Mersive Solstice and Nitro. The documentation on using these tools via commandline is frequently lacking and frustrating to work out.
Additional utilities like cleanup tools are pretty common with applications. Having an integrated checkbox for "run cleanup utility before install" or other options would save a lot of time in these cases and make it easier to get PMP integrated when just getting started.