Use Powershell to install all the MSI installers then have Powershell move the ProductLicenses.xml key file to C:\ProgramData\Quest Software instead of using the questkey.reg
If SCCM has a task to allow an admin to copy files over to a client machine this could also work. Even if it doesn't specifically have a "copy file" task, it does have the command-line and power shell tasks which will accomplish the same goal.
You can create the QuestKey.reg file ahead of time and have SCCM copy the file to the client machine after the installation has finished.
Then, you should be able to instruct SCCM to execute a command-line command to import the registry settings, as stated in the following pages:
Run Command Line task Sequnce Step (Microsoft article)
Task Sequence Steps in Configuration Manager (Microsoft article)
Alternatively, you should be able to execute a Powershell task to update the registry, as outlined here:
Use PowerShell to Easily Modify Registry Property Values (Microsoft article)